{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# V(D)J clustering\n",
"\n",
"On the topic of finding clones/clonotypes, there are many ways used for clustering BCRs, almost all involving some measure based on sequence similarity. There are also a lot of very well established guidelines and criterias maintained by the BCR community. For example, *immcantation* uses a number of model-based [methods](https://changeo.readthedocs.io/en/stable/methods/clustering.html) [[Gupta2015]](https://academic.oup.com/bioinformatics/article/31/20/3356/195677) to group clones based on the distribution of length-normalised junctional hamming distance while others use the whole BCR V(D)J sequence to define clones as shown in this paper [[Bashford-Rogers2019]](https://www.nature.com/articles/s41586-019-1595-3)."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"import os\n",
"import scanpy as sc\n",
"import dandelion as ddl\n",
"\n",
"ddl.set_backend(\"base\")\n",
"\n",
"os.chdir(\"dandelion_tutorial\")\n",
"sc.settings.verbosity = 3"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"scrolled": true
},
"outputs": [
{
"data": {
"text/plain": [
"Dandelion class object with n_obs = 2493 and n_contigs = 7355\n",
" data: 'sequence_id', 'sequence', 'rev_comp', 'productive', 'v_call', 'd_call', 'j_call', 'sequence_alignment', 'germline_alignment', 'junction', 'junction_aa', 'v_cigar', 'd_cigar', 'j_cigar', 'stop_codon', 'vj_in_frame', 'locus', 'c_call', 'junction_length', 'np1_length', 'np2_length', 'v_sequence_start', 'v_sequence_end', 'v_germline_start', 'v_germline_end', 'd_sequence_start', 'd_sequence_end', 'd_germline_start', 'd_germline_end', 'j_sequence_start', 'j_sequence_end', 'j_germline_start', 'j_germline_end', 'v_score', 'v_identity', 'v_support', 'd_score', 'd_identity', 'd_support', 'j_score', 'j_identity', 'j_support', 'fwr1', 'fwr2', 'fwr3', 'fwr4', 'cdr1', 'cdr2', 'cdr3', 'cell_id', 'consensus_count', 'umi_count', 'v_call_10x', 'd_call_10x', 'j_call_10x', 'junction_10x', 'junction_10x_aa', 'j_support_igblastn', 'j_score_igblastn', 'j_call_igblastn', 'j_call_blastn', 'j_identity_blastn', 'j_alignment_length_blastn', 'j_number_of_mismatches_blastn', 'j_number_of_gap_openings_blastn', 'j_sequence_start_blastn', 'j_sequence_end_blastn', 'j_germline_start_blastn', 'j_germline_end_blastn', 'j_support_blastn', 'j_score_blastn', 'j_sequence_alignment_blastn', 'j_germline_alignment_blastn', 'j_source', 'd_support_igblastn', 'd_score_igblastn', 'd_call_igblastn', 'd_call_blastn', 'd_identity_blastn', 'd_alignment_length_blastn', 'd_number_of_mismatches_blastn', 'd_number_of_gap_openings_blastn', 'd_sequence_start_blastn', 'd_sequence_end_blastn', 'd_germline_start_blastn', 'd_germline_end_blastn', 'd_support_blastn', 'd_score_blastn', 'd_sequence_alignment_blastn', 'd_germline_alignment_blastn', 'd_source', 'v_call_genotyped', 'germline_alignment_d_mask', 'sample_id', 'c_sequence_alignment', 'c_germline_alignment', 'c_sequence_start', 'c_sequence_end', 'c_score', 'c_identity', 'c_call_10x', 'junction_aa_length', 'fwr1_aa', 'fwr2_aa', 'fwr3_aa', 'fwr4_aa', 'cdr1_aa', 'cdr2_aa', 'cdr3_aa', 'sequence_alignment_aa', 'v_sequence_alignment_aa', 'd_sequence_alignment_aa', 'j_sequence_alignment_aa', 'complete_vdj', 'j_call_multimappers', 'j_call_multiplicity', 'j_call_sequence_start_multimappers', 'j_call_sequence_end_multimappers', 'j_call_support_multimappers', 'mu_count', 'ambiguous', 'extra', 'rearrangement_status'\n",
" metadata: 'sample_id', 'locus_VDJ', 'locus_VJ', 'productive_VDJ', 'productive_VJ', 'v_call_VDJ', 'd_call_VDJ', 'j_call_VDJ', 'v_call_VJ', 'j_call_VJ', 'c_call_VDJ', 'c_call_VJ', 'junction_VDJ', 'junction_VJ', 'junction_aa_VDJ', 'junction_aa_VJ', 'v_call_B_VDJ', 'd_call_B_VDJ', 'j_call_B_VDJ', 'v_call_B_VJ', 'j_call_B_VJ', 'c_call_B_VDJ', 'c_call_B_VJ', 'productive_B_VDJ', 'productive_B_VJ', 'umi_count_B_VDJ', 'umi_count_B_VJ', 'v_call_VDJ_main', 'v_call_VJ_main', 'd_call_VDJ_main', 'j_call_VDJ_main', 'j_call_VJ_main', 'c_call_VDJ_main', 'c_call_VJ_main', 'v_call_B_VDJ_main', 'd_call_B_VDJ_main', 'j_call_B_VDJ_main', 'v_call_B_VJ_main', 'j_call_B_VJ_main', 'isotype', 'isotype_status', 'locus_status', 'chain_status', 'rearrangement_status_VDJ', 'rearrangement_status_VJ'"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# read in the previously saved file\n",
"vdj = ddl.read_h5ddl(\"dandelion_results.h5ddl\")\n",
"vdj"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"AnnData object with n_obs × n_vars = 25057 × 1308\n",
" obs: 'sample_id', 'n_genes', 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt', 'gmm_pct_count_clusters_keep', 'scrublet_score', 'is_doublet', 'filter_rna', 'has_contig', 'locus_VDJ', 'locus_VJ', 'productive_VDJ', 'productive_VJ', 'v_call_VDJ', 'd_call_VDJ', 'j_call_VDJ', 'v_call_VJ', 'j_call_VJ', 'c_call_VDJ', 'c_call_VJ', 'junction_VDJ', 'junction_VJ', 'junction_aa_VDJ', 'junction_aa_VJ', 'v_call_B_VDJ', 'd_call_B_VDJ', 'j_call_B_VDJ', 'v_call_B_VJ', 'j_call_B_VJ', 'c_call_B_VDJ', 'c_call_B_VJ', 'productive_B_VDJ', 'productive_B_VJ', 'umi_count_B_VDJ', 'umi_count_B_VJ', 'v_call_VDJ_main', 'v_call_VJ_main', 'd_call_VDJ_main', 'j_call_VDJ_main', 'j_call_VJ_main', 'c_call_VDJ_main', 'c_call_VJ_main', 'v_call_B_VDJ_main', 'd_call_B_VDJ_main', 'j_call_B_VDJ_main', 'v_call_B_VJ_main', 'j_call_B_VJ_main', 'isotype', 'isotype_status', 'locus_status', 'chain_status', 'rearrangement_status_VDJ', 'rearrangement_status_VJ', 'leiden'\n",
" var: 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'\n",
" uns: 'chain_status_colors', 'hvg', 'leiden', 'leiden_colors', 'log1p', 'neighbors', 'pca', 'sample_id_colors', 'umap'\n",
" obsm: 'X_pca', 'X_umap'\n",
" varm: 'PCs'\n",
" obsp: 'connectivities', 'distances'"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"adata = sc.read_h5ad(\"adata.h5ad\")\n",
"adata"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Finding clones\n",
"\n",
"The following is *dandelion*'s implementation of a rather conventional method to define clones, `ddl.tl.find_clones`. \n",
"\n",
"\n",
"\n",
"Clone definition criterion\n",
" \n",
"Clone definition is based on the following criterion: I. Identical V- and J-gene usage in the VDJ chain (IGH/TRB/TRD).II. Identical CDR3 junctional/CDR3 sequence length in the VDJ chain.III. VDJ chain junctional/CDR3 sequences attains a minimum of % sequence similarity, based on hamming distance. The similarity cut-off is tunable (default is 85%; change to 100% if analyzing TCR data).IV. VJ chain (IGK/IGL/TRA/TRG) usage. If cells within clones use different VJ chains, the clone will be split following the same conditions for VDJ chains in (1-3) as above.\n",
"
"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### (Optional) Simplifying annotation calls.\n",
"This is an optional step to simplify the annotation calls. The `vdj.simplify()` will reduce the complexity of the gene names and strip the alleles. This impacts on how clones are defined (using simpler v/j calls) and also visualiation."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.microsoft.datawrangler.viewer.v0+json": {
"columns": [
{
"name": "sequence_id",
"rawType": "object",
"type": "string"
},
{
"name": "v_call_genotyped",
"rawType": "object",
"type": "string"
},
{
"name": "j_call",
"rawType": "object",
"type": "string"
},
{
"name": "c_call",
"rawType": "object",
"type": "string"
}
],
"ref": "793e7974-52a1-48ba-b3a8-af110670cda9",
"rows": [
[
"sc5p_v2_hs_PBMC_10k_b_AAACCTGTCATATCGG_contig_1",
"IGKV1-33*01,IGKV1D-33*01",
"IGKJ4*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACCTGTCCGTTGTC_contig_2",
"IGHV1-69*01,IGHV1-69D*01",
"IGHJ3*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACCTGTCCGTTGTC_contig_1",
"IGKV1-8*01",
"IGKJ1*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACCTGTCGAGAACG_contig_1",
"IGLV5-45*02",
"IGLJ3*02",
"IGLC3"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACCTGTCGAGAACG_contig_2",
"IGHV1-2*02",
"IGHJ3*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACCTGTCTTGAGAC_contig_2",
"IGHV5-51*03",
"IGHJ3*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACCTGTCTTGAGAC_contig_1",
"IGKV1D-8*01",
"IGKJ2*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACGGGAGCGACGTA_contig_1",
"IGHV4-4*07",
"IGHJ3*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACGGGAGCGACGTA_contig_2",
"IGLV3-19*01",
"IGLJ2*01,IGLJ3*01",
"IGLC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACGGGAGCGACGTA_contig_3",
"IGLV7-46*01",
"IGLJ3*02",
"IGLC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACGGGCACTGTTAG_contig_2",
"IGHV4-39*01",
"IGHJ3*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACGGGCACTGTTAG_contig_1",
"IGLV3-21*04",
"IGLJ2*01,IGLJ3*01",
"IGLC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACGGGCACTGTTAG_contig_3",
"IGHV3-7*01",
"IGHJ3*02",
"IGHD"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGATGAGGATGCGT_contig_2",
"IGKV2-28*01,IGKV2D-28*01",
"IGKJ2*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGATGAGGATGCGT_contig_1",
"IGHV3-30*02",
"IGHJ4*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGATGGTACTTCTT_contig_2",
"IGKV1-5*03",
"IGKJ3*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGATGGTACTTCTT_contig_1",
"IGHV2-5*02",
"IGHJ3*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGATGGTACTTCTT_contig_3",
"IGLV2-11*01",
"IGLJ2*01,IGLJ3*01",
"IGLC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGATGGTCGAATCT_contig_1",
"IGLV6-57*03",
"IGLJ2*01,IGLJ3*01",
"IGLC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGATGGTCGAATCT_contig_2",
"IGHV3-15*01",
"IGHJ4*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGATGGTGAGGGAG_contig_2",
"IGLV2-14*01,IGLV2-14*03",
"IGLJ3*02",
"IGLC3"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGATGGTGAGGGAG_contig_1",
"IGHV4-61*02",
"IGHJ6*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGATGGTGAGGGAG_contig_3",
"IGHV3-7*01",
"IGHJ4*02",
"IGHD"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGTAGCAGATCCAT_contig_1",
"IGKV1-27*01",
"IGKJ3*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGTAGCAGATCCAT_contig_2",
"IGHV1-2*02",
"IGHJ6*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGTAGCAGATCCAT_contig_3",
"IGKV1D-8*01",
"IGKJ1*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGTAGGTACAAGTA_contig_1",
"IGKV1-5*03",
"IGKJ1*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGTAGGTACAAGTA_contig_2",
"IGHV2-5*02",
"IGHJ3*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACACGTAGACACGAC_contig_2",
"IGKV1-39*01,IGKV1D-39*01",
"IGKJ2*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACACGTAGACACGAC_contig_1",
"IGHV3-7*01",
"IGHJ4*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACACGTCACAGACAG_contig_1",
"IGHV1-8*01",
"IGHJ3*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACACGTCACAGACAG_contig_2",
"IGKV3-20*01",
"IGKJ1*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACACGTGTACCGTAT_contig_1",
"IGHV3-9*01",
"IGHJ3*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACACGTGTACCGTAT_contig_2",
"IGKV4-1*01",
"IGKJ1*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACACGTTCCCTTGTG_contig_2",
"IGKV3-20*01",
"IGKJ2*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACACGTTCCCTTGTG_contig_1",
"IGHV3-9*01",
"IGHJ4*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACACGTTCCCTTGTG_contig_3",
"IGHV3-49*03,IGHV3-49*04",
"IGHJ4*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCATGCAAGCTGTT_contig_2",
"IGLV2-14*01,IGLV2-14*03",
"IGLJ1*01",
"IGLC1"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCATGCAAGCTGTT_contig_1",
"IGHV3-33*01",
"IGHJ6*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCATGTCAGTCCCT_contig_2",
"IGLV2-14*01,IGLV2-14*03",
"IGLJ2*01,IGLJ3*01",
"IGLC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCATGTCAGTCCCT_contig_1",
"IGHV3-49*04",
"IGHJ3*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCATGTCCAAGTAC_contig_2",
"IGKV3-20*01",
"IGKJ3*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCATGTCCAAGTAC_contig_1",
"IGHV4-4*07",
"IGHJ6*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCATGTCTAGCACA_contig_2",
"IGLV1-47*01",
"IGLJ3*02",
"IGLC3"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCATGTCTAGCACA_contig_1",
"IGHV4-30-2*01",
"IGHJ6*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCGCGCAACACCTA_contig_1",
"IGKV1-39*01,IGKV1D-39*01",
"IGKJ2*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCGCGCAACACCTA_contig_3",
"IGHV3-9*01",
"IGHJ3*02",
"IGHM"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCGCGCAACACCTA_contig_2",
"IGKV3-20*01",
"IGKJ5*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCGCGCAAGCTGAG_contig_4",
"IGKV2D-29*01",
"IGKJ4*01",
"IGKC"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCGCGCAAGCTGAG_contig_1",
"IGLV8-61*01",
"IGLJ2*01,IGLJ3*01",
"IGLC"
]
],
"shape": {
"columns": 3,
"rows": 7355
}
},
"text/html": [
"\n",
"\n",
"
\n",
" \n",
" \n",
" v_call_genotyped \n",
" j_call \n",
" c_call \n",
" \n",
" \n",
" sequence_id \n",
" \n",
" \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCATATCGG_contig_1 \n",
" IGKV1-33*01,IGKV1D-33*01 \n",
" IGKJ4*01 \n",
" IGKC \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCCGTTGTC_contig_2 \n",
" IGHV1-69*01,IGHV1-69D*01 \n",
" IGHJ3*02 \n",
" IGHM \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCCGTTGTC_contig_1 \n",
" IGKV1-8*01 \n",
" IGKJ1*01 \n",
" IGKC \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCGAGAACG_contig_1 \n",
" IGLV5-45*02 \n",
" IGLJ3*02 \n",
" IGLC3 \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCGAGAACG_contig_2 \n",
" IGHV1-2*02 \n",
" IGHJ3*02 \n",
" IGHM \n",
" \n",
" \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTCCTCTCGACAGCC_contig_1 \n",
" IGHV1-46*01 \n",
" IGHJ5*02 \n",
" IGHM \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTGCGCCATACCATG_contig_2 \n",
" IGHV1-69*01,IGHV1-69D*01 \n",
" IGHJ6*02 \n",
" IGHM \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTGCGCCATACCATG_contig_1 \n",
" IGLV1-47*01 \n",
" IGLJ3*02 \n",
" IGLC3 \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTGGTTGTAGGCATG_contig_2 \n",
" IGLV2-11*01 \n",
" IGLJ2*01,IGLJ3*01,IGLJ3*02 \n",
" IGLC \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTGGTTGTAGGCATG_contig_1 \n",
" IGHV3-23*01,IGHV3-23D*01 \n",
" IGHJ4*02 \n",
" IGHM \n",
" \n",
" \n",
"
\n",
"
7355 rows × 3 columns
\n",
"
\n",
"\n",
"
\n",
" \n",
" \n",
" v_call_genotyped \n",
" j_call \n",
" c_call \n",
" \n",
" \n",
" sequence_id \n",
" \n",
" \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCATATCGG_contig_1 \n",
" IGKV1-33 \n",
" IGKJ4 \n",
" IGKC \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCCGTTGTC_contig_2 \n",
" IGHV1-69 \n",
" IGHJ3 \n",
" IGHM \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCCGTTGTC_contig_1 \n",
" IGKV1-8 \n",
" IGKJ1 \n",
" IGKC \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCGAGAACG_contig_1 \n",
" IGLV5-45 \n",
" IGLJ3 \n",
" IGLC3 \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCGAGAACG_contig_2 \n",
" IGHV1-2 \n",
" IGHJ3 \n",
" IGHM \n",
" \n",
" \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTCCTCTCGACAGCC_contig_1 \n",
" IGHV1-46 \n",
" IGHJ5 \n",
" IGHM \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTGCGCCATACCATG_contig_2 \n",
" IGHV1-69 \n",
" IGHJ6 \n",
" IGHM \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTGCGCCATACCATG_contig_1 \n",
" IGLV1-47 \n",
" IGLJ3 \n",
" IGLC3 \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTGGTTGTAGGCATG_contig_2 \n",
" IGLV2-11 \n",
" IGLJ2 \n",
" IGLC \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTGGTTGTAGGCATG_contig_1 \n",
" IGHV3-23 \n",
" IGHJ4 \n",
" IGHM \n",
" \n",
" \n",
"
\n",
"
7355 rows × 3 columns
\n",
"
\n",
"\n",
"Clonotype definition criterion\n",
"\n",
"The `clone_id` follows an `VDJ_{A}_{B}_{C}_VJ_{D}_{E}_{F}` format and largely reflects the conditions above where:\n",
"\n",
" {A} indicates if the contigs use the same V and J genes in the VDJ chain.\n",
" \n",
" {B} indicates if junctional/CDR3 sequences are equal in length in the VDJ chain.\n",
" \n",
" {C} indicates if clones are split based on junctional/CDR3 hamming distance threshold (for VDJ chain).\n",
" \n",
" {D} indicates if the contigs use the same V and J genes in the VJ chain.\n",
" \n",
" {E} indicates if junctional/CDR3 sequences are equal in length in the VJ chain.\n",
" \n",
" {F} indicates if clones are split based on junctional/CDR3 hamming distance threshold (for VJ chain).\n",
"\n",
"
\n",
"\n",
"Also, to prevent issues with clonotype ids matching between B cells and T cells, there will be a prefix added to the `clone_id` to reflect whether or not it's a `B`, `abT` or `gdT` clone.\n",
"\n",
"Therefor, a complete B cell clonotype id will look something like:\n",
"\n",
"`B_VDJ_1_1_2_VJ_2_1_1`\n",
"\n",
"For an `Orphan VDJ`, it would be `B_VDJ_1_1_2`.\n",
"\n",
"For an `Orphan VJ`, it would be `B_VJ_2_1_1`.\n",
"\n",
"The individual numbers in the clonotype id do not have any meaning on their own, other than to indicate whether or not the conditions were met. For example, a `1` in the first position indicates that all contigs in that clone use the same V and J genes in the VDJ chain, while a `2` indicates that there that clone uses a different set of V/J genes.\n",
"\n",
"There are different defaults depending on the type of receptor data being analysed. For BCR data, the default identity threshold is set to `0.85` (i.e. 85% similarity based on hamming distance) while for TCR data, the default is set to `1.0` (i.e. 100% similarity). BCR uses `junction_aa` (amino acid) as the default key for calculating hamming distance while TCR uses `junction` (nucleotide) as default. These two parameters can be changed via the `identity` and `key` options respectively, which accepts a dictionary for each receptor type like so:\n",
"\n",
"```python\n",
"ddl.tl.find_clones(vdj, \n",
" identity = {'ig': 0.85, 'tr-ab': 1.0, 'tr-gd': 1.0}, \n",
" key = {'ig': 'junction_aa', 'tr-ab': 'junction', 'tr-gd': 'junction'}\n",
")\n",
"```\n",
"\n",
"This also means that `ddl.tl.find_clones` can be used for data containing both BCR and TCR data in the same object and the appropriate parameters will be applied to each receptor type accordingly.\n",
"\n",
"\n",
"There is also an alternate column called `clone_id_rank` which is a simplified numerical version of the `clone_id` which corresponds to the size of the clonotype - `1` is the largest clonotype, `2` is the second largest, and so on. Numbering is done separately for each receptor type if there are multiple receptor types in the data, i.e. it would look like `B_1`, `B_2`, `abT_1`, etc. There is a separate tutorial on handling multi-receptor data at [here](https://dandelion-tutorials.readthedocs.io/en/latest/multi_receptor_analysis.html) that will go into more details.\n"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.microsoft.datawrangler.viewer.v0+json": {
"columns": [
{
"name": "index",
"rawType": "object",
"type": "string"
},
{
"name": "clone_id",
"rawType": "object",
"type": "string"
},
{
"name": "clone_id_rank",
"rawType": "category",
"type": "unknown"
},
{
"name": "sample_id",
"rawType": "object",
"type": "string"
},
{
"name": "locus_VDJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "locus_VJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "productive_VDJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "productive_VJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "v_call_VDJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "d_call_VDJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "j_call_VDJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "v_call_VJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "j_call_VJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "c_call_VDJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "c_call_VJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "junction_VDJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "junction_VJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "junction_aa_VDJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "junction_aa_VJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "v_call_B_VDJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "d_call_B_VDJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "j_call_B_VDJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "v_call_B_VJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "j_call_B_VJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "c_call_B_VDJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "c_call_B_VJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "productive_B_VDJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "productive_B_VJ",
"rawType": "object",
"type": "unknown"
},
{
"name": "umi_count_B_VDJ",
"rawType": "float64",
"type": "float"
},
{
"name": "umi_count_B_VJ",
"rawType": "float64",
"type": "float"
},
{
"name": "v_call_VDJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "v_call_VJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "d_call_VDJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "j_call_VDJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "j_call_VJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "c_call_VDJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "c_call_VJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "v_call_B_VDJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "d_call_B_VDJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "j_call_B_VDJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "v_call_B_VJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "j_call_B_VJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "isotype",
"rawType": "object",
"type": "unknown"
},
{
"name": "isotype_status",
"rawType": "object",
"type": "unknown"
},
{
"name": "locus_status",
"rawType": "object",
"type": "string"
},
{
"name": "chain_status",
"rawType": "object",
"type": "string"
},
{
"name": "rearrangement_status_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "rearrangement_status_VJ",
"rawType": "object",
"type": "string"
}
],
"ref": "22b82e80-1f2a-410e-b877-462e7929e1d0",
"rows": [
[
"sc5p_v2_hs_PBMC_10k_b_AAACCTGTCATATCGG",
"B_VJ_127_2_2",
"135",
"sc5p_v2_hs_PBMC_10k_b",
null,
"IGK",
null,
"T",
null,
null,
null,
"IGKV1-33",
"IGKJ4",
null,
"IGKC",
null,
"TGTCAACAATATGACGAACTTCCCGTCACTTTC",
null,
"CQQYDELPVTF",
null,
null,
null,
"IGKV1-33",
"IGKJ4",
null,
"IGKC",
null,
"T",
null,
"68.0",
"None",
"IGKV1-33",
"None",
"None",
"IGKJ4",
"None",
"IGKC",
"None",
"None",
"None",
"IGKV1-33",
"IGKJ4",
null,
null,
"Orphan IGK",
"Orphan VJ",
"None",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACCTGTCCGTTGTC",
"B_VDJ_151_4_1_VJ_151_2_1",
"2196",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV1-69",
"IGHD3-22",
"IGHJ3",
"IGKV1-8",
"IGKJ1",
"IGHM",
"IGKC",
"TGTGCGACTACGTATTACTATGATAGTAGTGGTTATTACCAGAATGATGCTTTTGATATCTGG",
"TGTCAACAGTATTATAGTTACCCTCGGACGTTC",
"CATTYYYDSSGYYQNDAFDIW",
"CQQYYSYPRTF",
"IGHV1-69",
"IGHD3-22",
"IGHJ3",
"IGKV1-8",
"IGKJ1",
"IGHM",
"IGKC",
"T",
"T",
"51.0",
"43.0",
"IGHV1-69",
"IGKV1-8",
"IGHD3-22",
"IGHJ3",
"IGKJ1",
"IGHM",
"IGKC",
"IGHV1-69",
"IGHD3-22",
"IGHJ3",
"IGKV1-8",
"IGKJ1",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACCTGTCGAGAACG",
"B_VDJ_1_1_1_VJ_33_1_1",
"1750",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV1-2",
null,
"IGHJ3",
"IGLV5-45",
"IGLJ3",
"IGHM",
"IGLC3",
"TGTGCGAGAGAGATAGAGGGGGACGGTGTTTTTGAAATCTGG",
"TGTATGATTTGGCACAGCAGCGCTTGGGTGGTC",
"CAREIEGDGVFEIW",
"CMIWHSSAWVV",
"IGHV1-2",
null,
"IGHJ3",
"IGLV5-45",
"IGLJ3",
"IGHM",
"IGLC3",
"T",
"T",
"47.0",
"90.0",
"IGHV1-2",
"IGLV5-45",
"None",
"IGHJ3",
"IGLJ3",
"IGHM",
"IGLC3",
"IGHV1-2",
"None",
"IGHJ3",
"IGLV5-45",
"IGLJ3",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACCTGTCTTGAGAC",
"B_VDJ_152_4_2_VJ_84_1_1",
"1751",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV5-51",
null,
"IGHJ3",
"IGKV1D-8",
"IGKJ2",
"IGHM",
"IGKC",
"TGTGCGAGACATATCCGTGGGAACAGATTTGGCAATGATGCTTTTGATATCTGG",
"TGTCAACAGTATTATAGTTTCCCGTACACTTTT",
"CARHIRGNRFGNDAFDIW",
"CQQYYSFPYTF",
"IGHV5-51",
null,
"IGHJ3",
"IGKV1D-8",
"IGKJ2",
"IGHM",
"IGKC",
"T",
"T",
"80.0",
"22.0",
"IGHV5-51",
"IGKV1D-8",
"None",
"IGHJ3",
"IGKJ2",
"IGHM",
"IGKC",
"IGHV5-51",
"None",
"IGHJ3",
"IGKV1D-8",
"IGKJ2",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACGGGAGCGACGTA",
"B_VDJ_31_2_1_VJ_4_2_1",
"1752",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV4-4",
"IGHD6-13",
"IGHJ3",
"IGLV3-19",
"IGLJ2",
"IGHM",
"IGLC",
"TGTGCGAGAGTAGGCTATAGAGCAGCAGCTGGTACTGATGCTTTTGATATCTGG",
"TGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTC",
"CARVGYRAAAGTDAFDIW",
"CNSRDSSGNHVVF",
"IGHV4-4",
"IGHD6-13",
"IGHJ3",
"IGLV3-19",
"IGLJ2",
"IGHM",
"IGLC",
"T",
"T",
"18.0",
"14.0",
"IGHV4-4",
"IGLV3-19",
"IGHD6-13",
"IGHJ3",
"IGLJ2",
"IGHM",
"IGLC",
"IGHV4-4",
"IGHD6-13",
"IGHJ3",
"IGLV3-19",
"IGLJ2",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAACGGGCACTGTTAG",
"B_VDJ_18_2_1_VJ_59_4_1",
"1753",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV4-39",
"IGHD3-22",
"IGHJ3",
"IGLV3-21",
"IGLJ2",
"IGHM",
"IGLC",
"TGTGCGAGACGCCTCATTACTATGATAGAGGGAGGTGCTTTTGATATCTGG",
"TGTCAGGTGTGGGATAGTAGTAGTGATCATGTGGTATTC",
"CARRLITMIEGGAFDIW",
"CQVWDSSSDHVVF",
"IGHV4-39",
"IGHD3-22",
"IGHJ3",
"IGLV3-21",
"IGLJ2",
"IGHM",
"IGLC",
"T",
"T",
"26.0",
"18.0",
"IGHV4-39",
"IGLV3-21",
"IGHD3-22",
"IGHJ3",
"IGLJ2",
"IGHM",
"IGLC",
"IGHV4-39",
"IGHD3-22",
"IGHJ3",
"IGLV3-21",
"IGLJ2",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGATGAGGATGCGT",
"B_VDJ_51_10_5_VJ_77_3_1",
"1754",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV3-30",
null,
"IGHJ4",
"IGKV2-28",
"IGKJ2",
"IGHM",
"IGKC",
"TGTGCGAAAGTCATGATAGAACACCCATCGAACAGGGGCCACTTTGACTACTGG",
"TGCATGCAAGCTCTACAAACTCCGTACACTTTT",
"CAKVMIEHPSNRGHFDYW",
"CMQALQTPYTF",
"IGHV3-30",
null,
"IGHJ4",
"IGKV2-28",
"IGKJ2",
"IGHM",
"IGKC",
"T",
"T",
"30.0",
"59.0",
"IGHV3-30",
"IGKV2-28",
"None",
"IGHJ4",
"IGKJ2",
"IGHM",
"IGKC",
"IGHV3-30",
"None",
"IGHJ4",
"IGKV2-28",
"IGKJ2",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGATGGTCGAATCT",
"B_VDJ_171_12_4_VJ_183_1_1",
"1755",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV3-15",
"IGHD1-26",
"IGHJ4",
"IGLV6-57",
"IGLJ2",
"IGHM",
"IGLC",
"TGTACCACAGACGACGAAAAACGCCCCTATAGTGGGAGCTACCTCCCATTTGACTACTGG",
"TGTCAGTCTTATGATAGCAGCAATGTGGTATTC",
"CTTDDEKRPYSGSYLPFDYW",
"CQSYDSSNVVF",
"IGHV3-15",
"IGHD1-26",
"IGHJ4",
"IGLV6-57",
"IGLJ2",
"IGHM",
"IGLC",
"T",
"T",
"26.0",
"40.0",
"IGHV3-15",
"IGLV6-57",
"IGHD1-26",
"IGHJ4",
"IGLJ2",
"IGHM",
"IGLC",
"IGHV3-15",
"IGHD1-26",
"IGHJ4",
"IGLV6-57",
"IGLJ2",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGATGGTGAGGGAG",
"B_VDJ_101_10_3_VJ_178_3_1",
"1756",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV4-61",
"IGHD2-21",
"IGHJ6",
"IGLV2-14",
"IGLJ3",
"IGHM",
"IGLC3",
"TGTGCGAGAGAGACGACTCCCGTGGTGACTGCTTCCACATACTACTACTACTACGGTATGGACGTCTGG",
"TGCAGCTCATATACAAGCAGCAGCACTTGGGTGTTC",
"CARETTPVVTASTYYYYYGMDVW",
"CSSYTSSSTWVF",
"IGHV4-61",
"IGHD2-21",
"IGHJ6",
"IGLV2-14",
"IGLJ3",
"IGHM",
"IGLC3",
"T",
"T",
"15.0",
"54.0",
"IGHV4-61",
"IGLV2-14",
"IGHD2-21",
"IGHJ6",
"IGLJ3",
"IGHM",
"IGLC3",
"IGHV4-61",
"IGHD2-21",
"IGHJ6",
"IGLV2-14",
"IGLJ3",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGTAGCAGATCCAT",
"B_VDJ_34_11_1_VJ_158_2_1",
"1749",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV1-2",
"IGHD6-19",
"IGHJ6",
"IGKV1-27",
"IGKJ3",
"IGHM",
"IGKC",
"TGTGCGAGGGGGGGTCGTGTGTCAGTGGCTGTGTATTGGGACTACTACTACTACGGTATGGACGTCTGG",
"TGTCAAAAGTATAACAGTGCCCCATTCACTTTC",
"CARGGRVSVAVYWDYYYYGMDVW",
"CQKYNSAPFTF",
"IGHV1-2",
"IGHD6-19",
"IGHJ6",
"IGKV1-27",
"IGKJ3",
"IGHM",
"IGKC",
"T",
"T",
"42.0",
"70.0",
"IGHV1-2",
"IGKV1-27",
"IGHD6-19",
"IGHJ6",
"IGKJ3",
"IGHM",
"IGKC",
"IGHV1-2",
"IGHD6-19",
"IGHJ6",
"IGKV1-27",
"IGKJ3",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAAGTAGGTACAAGTA",
"B_VDJ_135_7_1_VJ_39_3_1",
"1757",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV2-5",
"IGHD3-9",
"IGHJ3",
"IGKV1-5",
"IGKJ1",
"IGHM",
"IGKC",
"TGTGCACACAGCGCCCAATATTACGATATTTTGACTGGTTATTATAAGGCGCCGTGGGGGGGTGCTTTTGATATCTGG",
"TGCCAACAGTATAATAGTTATTCGTGGACGTTC",
"CAHSAQYYDILTGYYKAPWGGAFDIW",
"CQQYNSYSWTF",
"IGHV2-5",
"IGHD3-9",
"IGHJ3",
"IGKV1-5",
"IGKJ1",
"IGHM",
"IGKC",
"T",
"T",
"34.0",
"49.0",
"IGHV2-5",
"IGKV1-5",
"IGHD3-9",
"IGHJ3",
"IGKJ1",
"IGHM",
"IGKC",
"IGHV2-5",
"IGHD3-9",
"IGHJ3",
"IGKV1-5",
"IGKJ1",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACACGTAGACACGAC",
"B_VDJ_70_8_7_VJ_95_2_1",
"1759",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV3-7",
"IGHD1-26",
"IGHJ4",
"IGKV1-39",
"IGKJ2",
"IGHM",
"IGKC",
"TGTGCGAGAGATGATTTCGGGGGAGCTACTTTTTATTCCTCTTTTGACTACTGG",
"TGTCAACAGAGTTACAGTACCCCGTACACTTTT",
"CARDDFGGATFYSSFDYW",
"CQQSYSTPYTF",
"IGHV3-7",
"IGHD1-26",
"IGHJ4",
"IGKV1-39",
"IGKJ2",
"IGHM",
"IGKC",
"T",
"T",
"33.0",
"43.0",
"IGHV3-7",
"IGKV1-39",
"IGHD1-26",
"IGHJ4",
"IGKJ2",
"IGHM",
"IGKC",
"IGHV3-7",
"IGHD1-26",
"IGHJ4",
"IGKV1-39",
"IGKJ2",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACACGTCACAGACAG",
"B_VDJ_148_3_1_VJ_164_5_1",
"1760",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV1-8",
"IGHD3-3",
"IGHJ3",
"IGKV3-20",
"IGKJ1",
"IGHM",
"IGKC",
"TGTGCGAGAGCCGCGAAGATTTTTGGAGTGGTTACCGCTTTTGATATCTGG",
"TGTCAGCAGTATGGTAGCTCACCGTGGACGTTC",
"CARAAKIFGVVTAFDIW",
"CQQYGSSPWTF",
"IGHV1-8",
"IGHD3-3",
"IGHJ3",
"IGKV3-20",
"IGKJ1",
"IGHM",
"IGKC",
"T",
"T",
"44.0",
"29.0",
"IGHV1-8",
"IGKV3-20",
"IGHD3-3",
"IGHJ3",
"IGKJ1",
"IGHM",
"IGKC",
"IGHV1-8",
"IGHD3-3",
"IGHJ3",
"IGKV3-20",
"IGKJ1",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACACGTTCCCTTGTG",
"B_VDJ_55_4_3_VJ_156_3_1",
"1761",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV3-9",
"IGHD6-19",
"IGHJ4",
"IGKV3-20",
"IGKJ2",
"IGHM",
"IGKC",
"TGTGTAAAAGACTATTCTACCAGTGGCTGGTACTACTTTGACTTCTGG",
"TGTCAGCAATATGGTAGCTCACTTCCGTACACTTTT",
"CVKDYSTSGWYYFDFW",
"CQQYGSSLPYTF",
"IGHV3-9",
"IGHD6-19",
"IGHJ4",
"IGKV3-20",
"IGKJ2",
"IGHM",
"IGKC",
"T",
"T",
"25.0",
"80.0",
"IGHV3-9",
"IGKV3-20",
"IGHD6-19",
"IGHJ4",
"IGKJ2",
"IGHM",
"IGKC",
"IGHV3-9",
"IGHD6-19",
"IGHJ4",
"IGKV3-20",
"IGKJ2",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCATGCAAGCTGTT",
"B_VDJ_133_2_1_VJ_68_2_1",
"1762",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV3-33",
"IGHD3-10",
"IGHJ6",
"IGLV2-14",
"IGLJ1",
"IGHM",
"IGLC1",
"TGTGCGAGAGATTGGGTTCGGGGAGTCAACGATATGGACGTCTGG",
"TGCAGCTCATATACAAGCAGCAGCACTCGGGTCTTC",
"CARDWVRGVNDMDVW",
"CSSYTSSSTRVF",
"IGHV3-33",
"IGHD3-10",
"IGHJ6",
"IGLV2-14",
"IGLJ1",
"IGHM",
"IGLC1",
"T",
"T",
"24.0",
"36.0",
"IGHV3-33",
"IGLV2-14",
"IGHD3-10",
"IGHJ6",
"IGLJ1",
"IGHM",
"IGLC1",
"IGHV3-33",
"IGHD3-10",
"IGHJ6",
"IGLV2-14",
"IGLJ1",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCATGTCAGTCCCT",
"B_VDJ_48_2_1_VJ_202_1_1",
"1763",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV3-49",
"IGHD1-26",
"IGHJ3",
"IGLV2-14",
"IGLJ2",
"IGHM",
"IGLC",
"TGTACTAGACCTCAACGGAAGTGGGAGCTACCCTACCCTGATGCTTTTGATATCTGG",
"TGCAGCTCATATACAAGCAGCAGCACTCTATTC",
"CTRPQRKWELPYPDAFDIW",
"CSSYTSSSTLF",
"IGHV3-49",
"IGHD1-26",
"IGHJ3",
"IGLV2-14",
"IGLJ2",
"IGHM",
"IGLC",
"T",
"T",
"23.0",
"74.0",
"IGHV3-49",
"IGLV2-14",
"IGHD1-26",
"IGHJ3",
"IGLJ2",
"IGHM",
"IGLC",
"IGHV3-49",
"IGHD1-26",
"IGHJ3",
"IGLV2-14",
"IGLJ2",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCATGTCCAAGTAC",
"B_VDJ_66_2_1_VJ_159_2_1",
"1764",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV4-4",
"IGHD2-2",
"IGHJ6",
"IGKV3-20",
"IGKJ3",
"IGHM",
"IGKC",
"TGTGCGAGAGTAGTACCAGCTGCCTTCTACGGTATGGACGTCTGG",
"TGTCAGCAGTATGGTAGCTCACTTTTCACTTTC",
"CARVVPAAFYGMDVW",
"CQQYGSSLFTF",
"IGHV4-4",
"IGHD2-2",
"IGHJ6",
"IGKV3-20",
"IGKJ3",
"IGHM",
"IGKC",
"T",
"T",
"16.0",
"55.0",
"IGHV4-4",
"IGKV3-20",
"IGHD2-2",
"IGHJ6",
"IGKJ3",
"IGHM",
"IGKC",
"IGHV4-4",
"IGHD2-2",
"IGHJ6",
"IGKV3-20",
"IGKJ3",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCATGTCTAGCACA",
"B_VDJ_146_5_1_VJ_149_2_1",
"1765",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV4-30-2",
"IGHD2-8",
"IGHJ6",
"IGLV1-47",
"IGLJ3",
"IGHM",
"IGLC3",
"TGTGCCGGGGGTTCGGGATATTGTACTAATGGTGTATGCTATCCCCGCGGGTTTGACTACTACTACGGTATGGACGTCTGG",
"TGTGCAGCATGGGATGACAGCCCGCCTTGGGTGTTC",
"CAGGSGYCTNGVCYPRGFDYYYGMDVW",
"CAAWDDSPPWVF",
"IGHV4-30-2",
"IGHD2-8",
"IGHJ6",
"IGLV1-47",
"IGLJ3",
"IGHM",
"IGLC3",
"T",
"T",
"17.0",
"35.0",
"IGHV4-30-2",
"IGLV1-47",
"IGHD2-8",
"IGHJ6",
"IGLJ3",
"IGHM",
"IGLC3",
"IGHV4-30-2",
"IGHD2-8",
"IGHJ6",
"IGLV1-47",
"IGLJ3",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACCGCGCATGAGCGA",
"B_VDJ_186_1_1_VJ_195_2_1",
"1758",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV6-1",
"IGHD6-6",
"IGHJ6",
"IGKV4-1",
"IGKJ2",
"IGHM",
"IGKC",
"TGTGCAAGAGATGAGGGAATAGCAGCTCGTACGAGAGGGGAGACCCACTACTACTACTACGGTATGGACGTCTGG",
"TGTCAGCAATATTATAGTACTCCGTACACTTTT",
"CARDEGIAARTRGETHYYYYGMDVW",
"CQQYYSTPYTF",
"IGHV6-1",
"IGHD6-6",
"IGHJ6",
"IGKV4-1",
"IGKJ2",
"IGHM",
"IGKC",
"T",
"T",
"34.0",
"59.0",
"IGHV6-1",
"IGKV4-1",
"IGHD6-6",
"IGHJ6",
"IGKJ2",
"IGHM",
"IGKC",
"IGHV6-1",
"IGHD6-6",
"IGHJ6",
"IGKV4-1",
"IGKJ2",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACGTTGGTCGTTGTA",
"B_VDJ_51_9_13_VJ_207_2_1",
"1747",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV3-30",
"IGHD5-18",
"IGHJ4",
"IGLV4-69",
"IGLJ3",
"IGHM",
"IGLC3",
"TGTGCGAAAGATGATACAGCTATGGTTACGGCCGATTTCTTTGACTACTGG",
"TGTCAGACCTGGGGCACTGGCATTTGGGTGTTC",
"CAKDDTAMVTADFFDYW",
"CQTWGTGIWVF",
"IGHV3-30",
"IGHD5-18",
"IGHJ4",
"IGLV4-69",
"IGLJ3",
"IGHM",
"IGLC3",
"T",
"T",
"14.0",
"11.0",
"IGHV3-30",
"IGLV4-69",
"IGHD5-18",
"IGHJ4",
"IGLJ3",
"IGHM",
"IGLC3",
"IGHV3-30",
"IGHD5-18",
"IGHJ4",
"IGLV4-69",
"IGLJ3",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACTCCCTCGTACCGG",
"B_VDJ_165_2_1_VJ_39_3_1",
"1738",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV2-26",
"IGHD5-24",
"IGHJ4",
"IGKV1-5",
"IGKJ1",
"IGHM",
"IGKC",
"TGTGCACGGACGCCGAGATGGCTACAATGTTTTGACTACTGG",
"TGCCAACAGTATAATAGTTATTCGTGGACGTTC",
"CARTPRWLQCFDYW",
"CQQYNSYSWTF",
"IGHV2-26",
"IGHD5-24",
"IGHJ4",
"IGKV1-5",
"IGKJ1",
"IGHM",
"IGKC",
"T",
"T",
"35.0",
"49.0",
"IGHV2-26",
"IGKV1-5",
"IGHD5-24",
"IGHJ4",
"IGKJ1",
"IGHM",
"IGKC",
"IGHV2-26",
"IGHD5-24",
"IGHJ4",
"IGKV1-5",
"IGKJ1",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACTCTTAGTAGCCGA",
"B_VDJ_51_6_1_VJ_103_2_1",
"1746",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV3-30",
"IGHD6-19",
"IGHJ4",
"IGLV6-57",
"IGLJ3",
"IGHG1",
"IGLC3",
"TGTGCGAGGGACCAGTGGCTGGCGTACTACTTTGACTACTGG",
"TGTCAGTCTTATGATAGCAGCAATCATTGGGTGTTC",
"CARDQWLAYYFDYW",
"CQSYDSSNHWVF",
"IGHV3-30",
"IGHD6-19",
"IGHJ4",
"IGLV6-57",
"IGLJ3",
"IGHG1",
"IGLC3",
"T",
"T",
"14.0",
"44.0",
"IGHV3-30",
"IGLV6-57",
"IGHD6-19",
"IGHJ4",
"IGLJ3",
"IGHG1",
"IGLC3",
"IGHV3-30",
"IGHD6-19",
"IGHJ4",
"IGLV6-57",
"IGLJ3",
"IgG",
"IgG",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACTCTTTCCGATATG",
"B_VDJ_184_2_1_VJ_56_1_1",
"1730",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV2-5",
"IGHD4-11",
"IGHJ4",
"IGKV2-30",
"IGKJ1",
"IGHM",
"IGKC",
"TGTGCACACAGATACTACAGTAACATTGACTACTGG",
"TGCATGCAAGGTACACACTGGCCGTGGACGTTC",
"CAHRYYSNIDYW",
"CMQGTHWPWTF",
"IGHV2-5",
"IGHD4-11",
"IGHJ4",
"IGKV2-30",
"IGKJ1",
"IGHM",
"IGKC",
"T",
"T",
"39.0",
"34.0",
"IGHV2-5",
"IGKV2-30",
"IGHD4-11",
"IGHJ4",
"IGKJ1",
"IGHM",
"IGKC",
"IGHV2-5",
"IGHD4-11",
"IGHJ4",
"IGKV2-30",
"IGKJ1",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACTGGTTCATTTGGG",
"B_VDJ_136_10_1_VJ_121_2_1",
"1731",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV3-74",
"IGHD3-22",
"IGHJ6",
"IGKV1-9",
"IGKJ3",
"IGHD",
"IGKC",
"TGTGCAAGAGATTGGGGTTACTATGATAGTAGTGGTTACTCCCCCAGGGGTTACTACTACTACTACGGTATGGACGTCTGG",
"TGTCAACAGCTTAATAGTTACTCTTTCACTTTC",
"CARDWGYYDSSGYSPRGYYYYYGMDVW",
"CQQLNSYSFTF",
"IGHV3-74",
"IGHD3-22",
"IGHJ6",
"IGKV1-9",
"IGKJ3",
"IGHD",
"IGKC",
"T",
"T",
"14.0",
"54.0",
"IGHV3-74",
"IGKV1-9",
"IGHD3-22",
"IGHJ6",
"IGKJ3",
"IGHD",
"IGKC",
"IGHV3-74",
"IGHD3-22",
"IGHJ6",
"IGKV1-9",
"IGKJ3",
"IgD",
"IgD",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACTTTCAGCTCAACT",
"B_VDJ_51_7_9_VJ_96_3_1",
"1732",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV3-30",
null,
"IGHJ4",
"IGKV3-15",
"IGKJ1",
"IGHM",
"IGKC",
"TGTGCGAAAGATCGGGTAGGATACGGTGACTACGTGGACTACTGG",
"TGTCAGCAGTATAATAACTGGCCTCCCTGGACGTTC",
"CAKDRVGYGDYVDYW",
"CQQYNNWPPWTF",
"IGHV3-30",
null,
"IGHJ4",
"IGKV3-15",
"IGKJ1",
"IGHM",
"IGKC",
"T",
"T",
"19.0",
"61.0",
"IGHV3-30",
"IGKV3-15",
"None",
"IGHJ4",
"IGKJ1",
"IGHM",
"IGKC",
"IGHV3-30",
"None",
"IGHJ4",
"IGKV3-15",
"IGKJ1",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AACTTTCCAATGTTGC",
"B_VDJ_131_1_1_VJ_65_3_1",
"1733",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV4-39",
null,
"IGHJ4",
"IGLV1-40",
"IGLJ1",
"IGHM",
"IGLC1",
"TGTGCGAGACTAGGCAGCAGCCCGTACTACTGG",
"TGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTC",
"CARLGSSPYYW",
"CQSYDSSLSGYVF",
"IGHV4-39",
null,
"IGHJ4",
"IGLV1-40",
"IGLJ1",
"IGHM",
"IGLC1",
"T",
"T",
"43.0",
"29.0",
"IGHV4-39",
"IGLV1-40",
"None",
"IGHJ4",
"IGLJ1",
"IGHM",
"IGLC1",
"IGHV4-39",
"None",
"IGHJ4",
"IGLV1-40",
"IGLJ1",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAGCCGCGTTTGTGTG",
"B_VDJ_86_1_1_VJ_89_1_1",
"1734",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV3-49",
null,
"IGHJ6",
"IGKV1D-8",
"IGKJ1",
"IGHM",
"IGKC",
"TGTACTAGATACTATGGGGACGTCTGG",
"TGTCAACAGTATTATAGTTTCCCGTGGACGTTC",
"CTRYYGDVW",
"CQQYYSFPWTF",
"IGHV3-49",
null,
"IGHJ6",
"IGKV1D-8",
"IGKJ1",
"IGHM",
"IGKC",
"T",
"T",
"14.0",
"59.0",
"IGHV3-49",
"IGKV1D-8",
"None",
"IGHJ6",
"IGKJ1",
"IGHM",
"IGKC",
"IGHV3-49",
"None",
"IGHJ6",
"IGKV1D-8",
"IGKJ1",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAGGAGCAGCTGCCCA",
"B_VDJ_132_11_1_VJ_18_1_1|B_VDJ_132_11_1_VJ_2_3_1",
"1735|1736",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL|IGL",
"T",
"T|T",
"IGHV3-23",
"IGHD2-15",
"IGHJ3",
"IGLV2-23|IGLV3-16",
"IGLJ1|IGLJ2",
"IGHD",
"IGLC1|IGLC",
"TGTGCGAAAGATTTCCATCGGCTAACCCTCCTTCGATATTGTAGTGGTGGTAGCTGCTACTCGGCTTTTGATATCTGG",
"TGCTGCTCATATGCAGGTAGTAGCACTTATGTCTTC|TGTCTATCAGCAGACAGCAGTGGTACTTATGTATTC",
"CAKDFHRLTLLRYCSGGSCYSAFDIW",
"CCSYAGSSTYVF|CLSADSSGTYVF",
"IGHV3-23",
"IGHD2-15",
"IGHJ3",
"IGLV2-23|IGLV3-16",
"IGLJ1|IGLJ2",
"IGHD",
"IGLC1|IGLC",
"T",
"T|T",
"13.0",
"90.0",
"IGHV3-23",
"IGLV2-23",
"IGHD2-15",
"IGHJ3",
"IGLJ1",
"IGHD",
"IGLC1",
"IGHV3-23",
"IGHD2-15",
"IGHJ3",
"IGLV2-23",
"IGLJ1",
"IgD",
"Multi",
"IGH + Extra VJ",
"Extra pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAGGAGCAGTTTGCGT",
"B_VDJ_51_11_2_VJ_86_4_1",
"1729",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV3-30",
"IGHD3-22",
"IGHJ4",
"IGLV3-25",
"IGLJ2",
"IGHM",
"IGLC",
"TGTGCGAAAGATCATTACTATGATAGTAGTGGTTATTACAGTGGTCTTGGCTACTGG",
"TGTCAATCAGCAGACAGCAGTGGTACTTATAGGGTGGTATTC",
"CAKDHYYDSSGYYSGLGYW",
"CQSADSSGTYRVVF",
"IGHV3-30",
"IGHD3-22",
"IGHJ4",
"IGLV3-25",
"IGLJ2",
"IGHM",
"IGLC",
"T",
"T",
"22.0",
"21.0",
"IGHV3-30",
"IGLV3-25",
"IGHD3-22",
"IGHJ4",
"IGLJ2",
"IGHM",
"IGLC",
"IGHV3-30",
"IGHD3-22",
"IGHJ4",
"IGLV3-25",
"IGLJ2",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAGGAGCCAGCCTTTC",
"B_VDJ_119_2_1_VJ_191_3_1",
"1737",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV1-24",
"IGHD2-2",
"IGHJ6",
"IGKV3-20",
"IGKJ4",
"IGHM",
"IGKC",
"TGTGCAACAGGCTTAGTAGTACCAGCTGCTATCCTCTATGGTATGGACGTCTGG",
"TGTCAGCAGTATGGTAGCTCACGAGGGCTCACTTTC",
"CATGLVVPAAILYGMDVW",
"CQQYGSSRGLTF",
"IGHV1-24",
"IGHD2-2",
"IGHJ6",
"IGKV3-20",
"IGKJ4",
"IGHM",
"IGKC",
"T",
"T",
"41.0",
"50.0",
"IGHV1-24",
"IGKV3-20",
"IGHD2-2",
"IGHJ6",
"IGKJ4",
"IGHM",
"IGKC",
"IGHV1-24",
"IGHD2-2",
"IGHJ6",
"IGKV3-20",
"IGKJ4",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAGGAGCGTAATCACC",
"B_VDJ_198_4_1_VJ_151_2_1",
"1739",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV4-34",
"IGHD4-17",
"IGHJ3",
"IGKV1-8",
"IGKJ1",
"IGHM",
"IGKC",
"TGTGCGAGTCGGGTGCATGGCTTAGTTACGGTGACTACGGGGGGAGCTTTTGATATCTGG",
"TGTCAACAGTATTATAGTTACCCTCCGGCGTTC",
"CASRVHGLVTVTTGGAFDIW",
"CQQYYSYPPAF",
"IGHV4-34",
"IGHD4-17",
"IGHJ3",
"IGKV1-8",
"IGKJ1",
"IGHM",
"IGKC",
"T",
"T",
"38.0",
"35.0",
"IGHV4-34",
"IGKV1-8",
"IGHD4-17",
"IGHJ3",
"IGKJ1",
"IGHM",
"IGKC",
"IGHV4-34",
"IGHD4-17",
"IGHJ3",
"IGKV1-8",
"IGKJ1",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAGGCAGAGTCATCCA",
"B_VDJ_187_10_1_VJ_68_3_4",
"1740",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV3-7",
null,
"IGHJ6",
"IGLV2-14",
"IGLJ1",
"IGHA1",
"IGLC1",
"TGCGCGAGGGGCGGTGCGGCGGTGACCACTTATTATTATTACTTCTACGGTATGGACGCCTGG",
"TGCTGCTCATATTCAAGCACCAATACACTATATGTCTTC",
"CARGGAAVTTYYYYFYGMDAW",
"CCSYSSTNTLYVF",
"IGHV3-7",
null,
"IGHJ6",
"IGLV2-14",
"IGLJ1",
"IGHA1",
"IGLC1",
"T",
"T",
"46.0",
"119.0",
"IGHV3-7",
"IGLV2-14",
"None",
"IGHJ6",
"IGLJ1",
"IGHA1",
"IGLC1",
"IGHV3-7",
"None",
"IGHJ6",
"IGLV2-14",
"IGLJ1",
"IgA",
"IgA",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAGGCAGAGTCGATAA",
"B_VDJ_47_8_3_VJ_100_1_1",
"1741",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV3-11",
"IGHD3-3",
"IGHJ4",
"IGLV1-36",
"IGLJ1",
"IGHM",
"IGLC1",
"TGTGCGAGAGATGGGAGTGGTTATCTCGAACAATACTACTTTGACTACTGG",
"TGTGCAGCATGGGATGACAGCCTGAATGGTTATGTCTTC",
"CARDGSGYLEQYYFDYW",
"CAAWDDSLNGYVF",
"IGHV3-11",
"IGHD3-3",
"IGHJ4",
"IGLV1-36",
"IGLJ1",
"IGHM",
"IGLC1",
"T",
"T",
"11.0",
"15.0",
"IGHV3-11",
"IGLV1-36",
"IGHD3-3",
"IGHJ4",
"IGLJ1",
"IGHM",
"IGLC1",
"IGHV3-11",
"IGHD3-3",
"IGHJ4",
"IGLV1-36",
"IGLJ1",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAGGCAGGTCTCCATC",
"B_VDJ_70_8_3_VJ_156_2_1",
"95",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV3-7",
"IGHD3-22",
"IGHJ4",
"IGKV3-20",
"IGKJ2",
"IGHM",
"IGKC",
"TGTGCGAGAGATGTACGAGTTTACTATGATAGTAGTGGTTACTCTGACTACTGG",
"TGTCAGCAGTATGGTAGCTCACCGTACACTTTT",
"CARDVRVYYDSSGYSDYW",
"CQQYGSSPYTF",
"IGHV3-7",
"IGHD3-22",
"IGHJ4",
"IGKV3-20",
"IGKJ2",
"IGHM",
"IGKC",
"T",
"T",
"15.0",
"20.0",
"IGHV3-7",
"IGKV3-20",
"IGHD3-22",
"IGHJ4",
"IGKJ2",
"IGHM",
"IGKC",
"IGHV3-7",
"IGHD3-22",
"IGHJ4",
"IGKV3-20",
"IGKJ2",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAGGTTCAGCAGATCG",
"B_VDJ_131_7_6_VJ_179_3_1",
"1742",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV4-39",
"IGHD1-26",
"IGHJ4",
"IGLV1-44",
"IGLJ1",
"IGHM",
"IGLC1",
"TGTGCGAGACTAATCAAGTATAGTGGGAGCTATGAGATGGTGGACTACTGG",
"TGTGCAGCATGGGATGACAGCCTGAATGGTTATTATGTCTTC",
"CARLIKYSGSYEMVDYW",
"CAAWDDSLNGYYVF",
"IGHV4-39",
"IGHD1-26",
"IGHJ4",
"IGLV1-44",
"IGLJ1",
"IGHM",
"IGLC1",
"T",
"T",
"30.0",
"35.0",
"IGHV4-39",
"IGLV1-44",
"IGHD1-26",
"IGHJ4",
"IGLJ1",
"IGHM",
"IGLC1",
"IGHV4-39",
"IGHD1-26",
"IGHJ4",
"IGLV1-44",
"IGLJ1",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AAGTCTGGTCTAACGT",
"B_VDJ_10_5_2_VJ_104_2_1",
"1743",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV3-21",
"IGHD3-22",
"IGHJ6",
"IGKV1-33",
"IGKJ3",
"IGHM",
"IGKC",
"TGTGCGAGAGGGGGATTTATTACTATGATAGGCTACGGTATGGACGTCTGG",
"TGTCAACAGTATGATAATCTCCCATTCACTTTC",
"CARGGFITMIGYGMDVW",
"CQQYDNLPFTF",
"IGHV3-21",
"IGHD3-22",
"IGHJ6",
"IGKV1-33",
"IGKJ3",
"IGHM",
"IGKC",
"T",
"T",
"13.0",
"50.0",
"IGHV3-21",
"IGKV1-33",
"IGHD3-22",
"IGHJ6",
"IGKJ3",
"IGHM",
"IGKC",
"IGHV3-21",
"IGHD3-22",
"IGHJ6",
"IGKV1-33",
"IGKJ3",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AATCCAGAGGCGTACA",
"B_VDJ_136_8_2_VJ_179_2_1",
"1744",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV3-74",
"IGHD2-15",
"IGHJ6",
"IGLV1-44",
"IGLJ1",
"IGHM",
"IGLC1",
"TGTGCAAGAGACCTGAGATGGTGTAGTGGTGGTAGCTGCTACGGGAACTACTACGGTATGGACGTCTGG",
"TGTGCAGCATGGGATGACAGCCTGAATGGTCAAGTCTTC",
"CARDLRWCSGGSCYGNYYGMDVW",
"CAAWDDSLNGQVF",
"IGHV3-74",
"IGHD2-15",
"IGHJ6",
"IGLV1-44",
"IGLJ1",
"IGHM",
"IGLC1",
"T",
"T",
"51.0",
"70.0",
"IGHV3-74",
"IGLV1-44",
"IGHD2-15",
"IGHJ6",
"IGLJ1",
"IGHM",
"IGLC1",
"IGHV3-74",
"IGHD2-15",
"IGHJ6",
"IGLV1-44",
"IGLJ1",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AATCCAGAGTTTAGGA",
"B_VDJ_51_7_2_VJ_195_3_1|B_VDJ_51_7_2_VJ_19_2_1",
"1745|1766",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL|IGK",
"T",
"T|T",
"IGHV3-30",
"IGHD6-13",
"IGHJ4",
"IGLV1-47|IGKV4-1",
"IGLJ2|IGKJ2",
"IGHM",
"IGLC|IGKC",
"TGTGCGAAAGATGATGGGGACGCAGCAGCTGGTTTAATCTACTGG",
"TGTGCAGCATGGGATGACAGCCTGAGTGGTGTGGTATTC|TGTCAGCAATATTATAGTACTCCCTTGTACACTTTT",
"CAKDDGDAAAGLIYW",
"CAAWDDSLSGVVF|CQQYYSTPLYTF",
"IGHV3-30",
"IGHD6-13",
"IGHJ4",
"IGLV1-47|IGKV4-1",
"IGLJ2|IGKJ2",
"IGHM",
"IGLC|IGKC",
"T",
"T|T",
"17.0",
"35.0",
"IGHV3-30",
"IGLV1-47",
"IGHD6-13",
"IGHJ4",
"IGLJ2",
"IGHM",
"IGLC",
"IGHV3-30",
"IGHD6-13",
"IGHJ4",
"IGLV1-47",
"IGLJ2",
"IgM",
"Multi",
"IGH + Extra VJ",
"Extra pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_AATCCAGCATCTATGG",
"B_VDJ_167_1_1_VJ_38_2_1",
"1767",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV3-43",
null,
"IGHJ4",
"IGLV1-51",
"IGLJ2",
"IGHM",
"IGLC",
"TGTGCAAAAGACGGGGGGGGGGAAGAGGCTTTAGAGCTACCAGACTACTGG",
"TGCGGAACATGGGATAGCAGCCTGAGTGCGGTGGTATTC",
"CAKDGGGEEALELPDYW",
"CGTWDSSLSAVVF",
"IGHV3-43",
null,
"IGHJ4",
"IGLV1-51",
"IGLJ2",
"IGHM",
"IGLC",
"T",
"T",
"26.0",
"33.0",
"IGHV3-43",
"IGLV1-51",
"None",
"IGHJ4",
"IGLJ2",
"IGHM",
"IGLC",
"IGHV3-43",
"None",
"IGHJ4",
"IGLV1-51",
"IGLJ2",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_ACACCAAGTGTAAGTA",
"B_VDJ_122_4_1_VJ_95_2_1",
"1768",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV4-30-2",
"IGHD6-19",
"IGHJ3",
"IGKV1-39",
"IGKJ2",
"IGHG4A",
"IGKC",
"TGTGCGAGAAAGGATAGCAGTGGTTCTGATGCTTTTGATTTGTGG",
"TGTCAACAGAGTTATAGTACCCCGTACACTTTT",
"CARKDSSGSDAFDLW",
"CQQSYSTPYTF",
"IGHV4-30-2",
"IGHD6-19",
"IGHJ3",
"IGKV1-39",
"IGKJ2",
"IGHG4A",
"IGKC",
"T",
"T",
"8.0",
"72.0",
"IGHV4-30-2",
"IGKV1-39",
"IGHD6-19",
"IGHJ3",
"IGKJ2",
"IGHG4A",
"IGKC",
"IGHV4-30-2",
"IGHD6-19",
"IGHJ3",
"IGKV1-39",
"IGKJ2",
"IgG",
"IgG",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_ACACCAATCATCGATG",
"B_VDJ_70_5_2_VJ_95_3_1",
"1778",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV3-7",
"IGHD5-18",
"IGHJ4",
"IGKV1-39",
"IGKJ2",
"IGHM",
"IGKC",
"TGTGCGAGAGATGTCGTACAGCTATGGTACCAAATTGACTACTGG",
"TGTCAACAGAGTTACAGTACCCCTCCGAACACTTTT",
"CARDVVQLWYQIDYW",
"CQQSYSTPPNTF",
"IGHV3-7",
"IGHD5-18",
"IGHJ4",
"IGKV1-39",
"IGKJ2",
"IGHM",
"IGKC",
"T",
"T",
"21.0",
"60.0",
"IGHV3-7",
"IGKV1-39",
"IGHD5-18",
"IGHJ4",
"IGKJ2",
"IGHM",
"IGKC",
"IGHV3-7",
"IGHD5-18",
"IGHJ4",
"IGKV1-39",
"IGKJ2",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_ACACCAATCTATCCCG",
"B_VDJ_149_3_2_VJ_174_1_1",
"1790",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV4-59",
"IGHD5-18",
"IGHJ5",
"IGKV1D-12",
"IGKJ5",
"IGHM",
"IGKC",
"TGTGCGAAATACGTGGATACAGCTATGAATCAGTTCGACCCCTGG",
"TGTCAACAGGCTAACAGTTTCCCGATCACCTTC",
"CAKYVDTAMNQFDPW",
"CQQANSFPITF",
"IGHV4-59",
"IGHD5-18",
"IGHJ5",
"IGKV1D-12",
"IGKJ5",
"IGHM",
"IGKC",
"T",
"T",
"20.0",
"28.0",
"IGHV4-59",
"IGKV1D-12",
"IGHD5-18",
"IGHJ5",
"IGKJ5",
"IGHM",
"IGKC",
"IGHV4-59",
"IGHD5-18",
"IGHJ5",
"IGKV1D-12",
"IGKJ5",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_ACACCCTCATATGAGA",
"B_VDJ_63_7_2_VJ_164_7_2",
"1791",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV1-69",
"IGHD3-22",
"IGHJ4",
"IGKV3-20",
"IGKJ1",
"IGHM",
"IGKC",
"TGTGCGAGAGGTCTTCATTACTATGATAGTAGTGGTCGTTCACTTTACTACTTTGACTACTGG",
"TGTCAGCAGTATGGTAGCTCACCTCCGGGACAGACGTTC",
"CARGLHYYDSSGRSLYYFDYW",
"CQQYGSSPPGQTF",
"IGHV1-69",
"IGHD3-22",
"IGHJ4",
"IGKV3-20",
"IGKJ1",
"IGHM",
"IGKC",
"T",
"T",
"17.0",
"44.0",
"IGHV1-69",
"IGKV3-20",
"IGHD3-22",
"IGHJ4",
"IGKJ1",
"IGHM",
"IGKC",
"IGHV1-69",
"IGHD3-22",
"IGHJ4",
"IGKV3-20",
"IGKJ1",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_ACACCCTTCAGAAATG",
"B_VDJ_51_2_1_VJ_96_2_1",
"1792",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV3-30",
null,
"IGHJ4",
"IGKV3-15",
"IGKJ1",
"IGHM",
"IGKC",
"TGTGCCAATCAGCCCCCCAGTCTCTATTGG",
"TGTCAGCAATATAATAACTGGCCCGGGACGTTC",
"CANQPPSLYW",
"CQQYNNWPGTF",
"IGHV3-30",
null,
"IGHJ4",
"IGKV3-15",
"IGKJ1",
"IGHM",
"IGKC",
"T",
"T",
"16.0",
"79.0",
"IGHV3-30",
"IGKV3-15",
"None",
"IGHJ4",
"IGKJ1",
"IGHM",
"IGKC",
"IGHV3-30",
"None",
"IGHJ4",
"IGKV3-15",
"IGKJ1",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_ACACCGGAGATCCGAG",
"B_VDJ_154_9_1_VJ_203_1_2",
"1793",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV3-48",
"IGHD3-16",
"IGHJ6",
"IGLV2-8",
"IGLJ1",
"IGHM",
"IGLC1",
"TGTGCGAGAGTGGGTTATGATTACGTTTGGGGGAGTTATCGTTATACGGGGGTTATGGACGTCTGG",
"TGCAGCTCATATGCAGGCAGCTCTTATGTCTTC",
"CARVGYDYVWGSYRYTGVMDVW",
"CSSYAGSSYVF",
"IGHV3-48",
"IGHD3-16",
"IGHJ6",
"IGLV2-8",
"IGLJ1",
"IGHM",
"IGLC1",
"T",
"T",
"19.0",
"44.0",
"IGHV3-48",
"IGLV2-8",
"IGHD3-16",
"IGHJ6",
"IGLJ1",
"IGHM",
"IGLC1",
"IGHV3-48",
"IGHD3-16",
"IGHJ6",
"IGLV2-8",
"IGLJ1",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_ACACTGACAGTCAGCC",
"B_VDJ_148_5_2_VJ_117_2_1",
"1794",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV1-8",
"IGHD3-22",
"IGHJ3",
"IGKV2-28",
"IGKJ4",
"IGHM",
"IGKC",
"TGTGCGAGAGGCCGCCCGTATTACTATGATAGTAGTGGTTACCCATATGATGCTTTTGATATCTGG",
"TGCATGCAAGCTCTACAAACCCCACTCACTTTC",
"CARGRPYYYDSSGYPYDAFDIW",
"CMQALQTPLTF",
"IGHV1-8",
"IGHD3-22",
"IGHJ3",
"IGKV2-28",
"IGKJ4",
"IGHM",
"IGKC",
"T",
"T",
"25.0",
"41.0",
"IGHV1-8",
"IGKV2-28",
"IGHD3-22",
"IGHJ3",
"IGKJ4",
"IGHM",
"IGKC",
"IGHV1-8",
"IGHD3-22",
"IGHJ3",
"IGKV2-28",
"IGKJ4",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_ACACTGAGTCAAAGCG",
"B_VDJ_35_11_4_VJ_80_2_1",
"1795",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV3-23",
"IGHD6-13",
"IGHJ4",
"IGKV2-30",
"IGKJ4",
"IGHM",
"IGKC",
"TGTGCGAAATTCGACATAGCAGCAGCTGATACGGGTAAAGGAGAGGACTACTGG",
"TGCATGCAAGGTACACACTGGCCTCCGCTCACTTTC",
"CAKFDIAAADTGKGEDYW",
"CMQGTHWPPLTF",
"IGHV3-23",
"IGHD6-13",
"IGHJ4",
"IGKV2-30",
"IGKJ4",
"IGHM",
"IGKC",
"T",
"T",
"12.0",
"48.0",
"IGHV3-23",
"IGKV2-30",
"IGHD6-13",
"IGHJ4",
"IGKJ4",
"IGHM",
"IGKC",
"IGHV3-23",
"IGHD6-13",
"IGHJ4",
"IGKV2-30",
"IGKJ4",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_ACACTGAGTTGTCTTT",
"B_VDJ_117_2_1_VJ_186_1_1",
"1796",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV4-34",
null,
"IGHJ5",
"IGLV2-23",
"IGLJ2",
"IGHM",
"IGLC",
"TGTGCGAGAGGCGGCGATCCCACCTGGTTCGACCCCTGG",
"TGCTGCTCATATGCAGGTAGTAGCATCGTGGTATTC",
"CARGGDPTWFDPW",
"CCSYAGSSIVVF",
"IGHV4-34",
null,
"IGHJ5",
"IGLV2-23",
"IGLJ2",
"IGHM",
"IGLC",
"T",
"T",
"37.0",
"31.0",
"IGHV4-34",
"IGLV2-23",
"None",
"IGHJ5",
"IGLJ2",
"IGHM",
"IGLC",
"IGHV4-34",
"None",
"IGHJ5",
"IGLV2-23",
"IGLJ2",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_ACAGCCGTCAGCATGT",
"B_VDJ_51_10_3_VJ_126_4_1",
"1797",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGK",
"T",
"T",
"IGHV3-30",
"IGHD2-21",
"IGHJ4",
"IGKV1-39",
"IGKJ4",
"IGHM",
"IGKC",
"TGTGCGAAGGAACGGGTGGTGACTGCTATTCCTGTGGTTATCTTTGACTACTGG",
"TGTCAACAGAGTTACAGTACCCCTAGGCTCACTTTC",
"CAKERVVTAIPVVIFDYW",
"CQQSYSTPRLTF",
"IGHV3-30",
"IGHD2-21",
"IGHJ4",
"IGKV1-39",
"IGKJ4",
"IGHM",
"IGKC",
"T",
"T",
"15.0",
"19.0",
"IGHV3-30",
"IGKV1-39",
"IGHD2-21",
"IGHJ4",
"IGKJ4",
"IGHM",
"IGKC",
"IGHV3-30",
"IGHD2-21",
"IGHJ4",
"IGKV1-39",
"IGKJ4",
"IgM",
"IgM",
"IGH + IGK",
"Single pair",
"standard",
"standard"
],
[
"sc5p_v2_hs_PBMC_10k_b_ACAGCTACACCACGTG",
"B_VDJ_47_5_1_VJ_65_3_1",
"1798",
"sc5p_v2_hs_PBMC_10k_b",
"IGH",
"IGL",
"T",
"T",
"IGHV3-11",
"IGHD4-17",
"IGHJ4",
"IGLV1-40",
"IGLJ1",
"IGHM",
"IGLC1",
"TGTGCGAGACCTTACGGTGACTACGCCTACTTTGACTACTGG",
"TGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTC",
"CARPYGDYAYFDYW",
"CQSYDSSLSGYVF",
"IGHV3-11",
"IGHD4-17",
"IGHJ4",
"IGLV1-40",
"IGLJ1",
"IGHM",
"IGLC1",
"T",
"T",
"52.0",
"68.0",
"IGHV3-11",
"IGLV1-40",
"IGHD4-17",
"IGHJ4",
"IGLJ1",
"IGHM",
"IGLC1",
"IGHV3-11",
"IGHD4-17",
"IGHJ4",
"IGLV1-40",
"IGLJ1",
"IgM",
"IgM",
"IGH + IGL",
"Single pair",
"standard",
"standard"
]
],
"shape": {
"columns": 47,
"rows": 2493
}
},
"text/html": [
"\n",
"\n",
"
\n",
" \n",
" \n",
" clone_id \n",
" clone_id_rank \n",
" sample_id \n",
" locus_VDJ \n",
" locus_VJ \n",
" productive_VDJ \n",
" productive_VJ \n",
" v_call_VDJ \n",
" d_call_VDJ \n",
" j_call_VDJ \n",
" ... \n",
" d_call_B_VDJ_main \n",
" j_call_B_VDJ_main \n",
" v_call_B_VJ_main \n",
" j_call_B_VJ_main \n",
" isotype \n",
" isotype_status \n",
" locus_status \n",
" chain_status \n",
" rearrangement_status_VDJ \n",
" rearrangement_status_VJ \n",
" \n",
" \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCATATCGG \n",
" B_VJ_127_2_2 \n",
" 135 \n",
" sc5p_v2_hs_PBMC_10k_b \n",
" None \n",
" IGK \n",
" None \n",
" T \n",
" None \n",
" None \n",
" None \n",
" ... \n",
" None \n",
" None \n",
" IGKV1-33 \n",
" IGKJ4 \n",
" None \n",
" None \n",
" Orphan IGK \n",
" Orphan VJ \n",
" None \n",
" standard \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCCGTTGTC \n",
" B_VDJ_151_4_1_VJ_151_2_1 \n",
" 2196 \n",
" sc5p_v2_hs_PBMC_10k_b \n",
" IGH \n",
" IGK \n",
" T \n",
" T \n",
" IGHV1-69 \n",
" IGHD3-22 \n",
" IGHJ3 \n",
" ... \n",
" IGHD3-22 \n",
" IGHJ3 \n",
" IGKV1-8 \n",
" IGKJ1 \n",
" IgM \n",
" IgM \n",
" IGH + IGK \n",
" Single pair \n",
" standard \n",
" standard \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCGAGAACG \n",
" B_VDJ_1_1_1_VJ_33_1_1 \n",
" 1750 \n",
" sc5p_v2_hs_PBMC_10k_b \n",
" IGH \n",
" IGL \n",
" T \n",
" T \n",
" IGHV1-2 \n",
" None \n",
" IGHJ3 \n",
" ... \n",
" None \n",
" IGHJ3 \n",
" IGLV5-45 \n",
" IGLJ3 \n",
" IgM \n",
" IgM \n",
" IGH + IGL \n",
" Single pair \n",
" standard \n",
" standard \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACCTGTCTTGAGAC \n",
" B_VDJ_152_4_2_VJ_84_1_1 \n",
" 1751 \n",
" sc5p_v2_hs_PBMC_10k_b \n",
" IGH \n",
" IGK \n",
" T \n",
" T \n",
" IGHV5-51 \n",
" None \n",
" IGHJ3 \n",
" ... \n",
" None \n",
" IGHJ3 \n",
" IGKV1D-8 \n",
" IGKJ2 \n",
" IgM \n",
" IgM \n",
" IGH + IGK \n",
" Single pair \n",
" standard \n",
" standard \n",
" \n",
" \n",
" sc5p_v2_hs_PBMC_10k_b_AAACGGGAGCGACGTA \n",
" B_VDJ_31_2_1_VJ_4_2_1 \n",
" 1752 \n",
" sc5p_v2_hs_PBMC_10k_b \n",
" IGH \n",
" IGL \n",
" T \n",
" T \n",
" IGHV4-4 \n",
" IGHD6-13 \n",
" IGHJ3 \n",
" ... \n",
" IGHD6-13 \n",
" IGHJ3 \n",
" IGLV3-19 \n",
" IGLJ2 \n",
" IgM \n",
" IgM \n",
" IGH + IGL \n",
" Single pair \n",
" standard \n",
" standard \n",
" \n",
" \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" ... \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTCCTCAGCGCTTAT \n",
" B_VDJ_173_5_6_VJ_47_1_1 \n",
" 895 \n",
" vdj_v1_hs_pbmc3_b \n",
" IGH \n",
" IGK \n",
" T \n",
" T \n",
" IGHV3-30 \n",
" IGHD4-17 \n",
" IGHJ6 \n",
" ... \n",
" IGHD4-17 \n",
" IGHJ6 \n",
" IGKV2-30 \n",
" IGKJ2 \n",
" IgM \n",
" IgM \n",
" IGH + IGK \n",
" Single pair \n",
" standard \n",
" standard \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTCCTCAGGGAAACA \n",
" B_VDJ_6_2_1_VJ_109_4_1 \n",
" 896 \n",
" vdj_v1_hs_pbmc3_b \n",
" IGH \n",
" IGK \n",
" T \n",
" T \n",
" IGHV4-61 \n",
" IGHD6-13 \n",
" IGHJ2 \n",
" ... \n",
" IGHD6-13 \n",
" IGHJ2 \n",
" IGKV1-39 \n",
" IGKJ1 \n",
" IgM \n",
" IgM \n",
" IGH + IGK \n",
" Single pair \n",
" standard \n",
" standard \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTCCTCTCGACAGCC \n",
" B_VDJ_16_5_1_VJ_95_2_1 \n",
" 897 \n",
" vdj_v1_hs_pbmc3_b \n",
" IGH \n",
" IGK \n",
" T \n",
" T \n",
" IGHV1-46 \n",
" IGHD2-15 \n",
" IGHJ5 \n",
" ... \n",
" IGHD2-15 \n",
" IGHJ5 \n",
" IGKV1-39 \n",
" IGKJ2 \n",
" IgM \n",
" IgM \n",
" IGH + IGK \n",
" Single pair \n",
" standard \n",
" standard \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTGCGCCATACCATG \n",
" B_VDJ_183_7_2_VJ_149_3_1 \n",
" 898 \n",
" vdj_v1_hs_pbmc3_b \n",
" IGH \n",
" IGL \n",
" T \n",
" T \n",
" IGHV1-69 \n",
" IGHD2-15 \n",
" IGHJ6 \n",
" ... \n",
" IGHD2-15 \n",
" IGHJ6 \n",
" IGLV1-47 \n",
" IGLJ3 \n",
" IgM \n",
" IgM \n",
" IGH + IGL \n",
" Single pair \n",
" standard \n",
" standard \n",
" \n",
" \n",
" vdj_v1_hs_pbmc3_b_TTTGGTTGTAGGCATG \n",
" B_VDJ_35_6_7_VJ_45_3_1 \n",
" 2598 \n",
" vdj_v1_hs_pbmc3_b \n",
" IGH \n",
" IGL \n",
" T \n",
" T \n",
" IGHV3-23 \n",
" None \n",
" IGHJ4 \n",
" ... \n",
" None \n",
" IGHJ4 \n",
" IGLV2-11 \n",
" IGLJ2 \n",
" IgM \n",
" IgM \n",
" IGH + IGL \n",
" Single pair \n",
" standard \n",
" standard \n",
" \n",
" \n",
"
\n",
"
2493 rows × 47 columns
\n",
"
\n",
"\n",
"Layout Method Updates\n",
"\n",
"Several new layout algorithm options are available:\n",
"\n",
"| Method | Description |\n",
"|---|---|\n",
"| `mod_fr` | Original Python modified Fruchterman-Reingold layout |\n",
"| `mod_fr2` | **New default.** Numba-accelerated FR layout (faster on CPU) |\n",
"| `mod_fr2_gpu` | PyTorch GPU-accelerated FR (auto-tiles for >100K nodes) |\n",
"| `mod_fr_bh` | Barnes-Hut O(N log N) CPU layout (scalable for large graphs) |\n",
"| `mod_fr_bh_gpu` | Barnes-Hut GPU layout (requires CUDA) |\n",
"| `fa2` | ForceAtlas2 (requires `fa2-modified`) |\n",
"\n",
"The `singleton_mass` parameter (default 0.5) controls the mass of isolated nodes in Barnes-Hut layouts. Lowering this reduces the repulsive force that singletons exert on connected components.\n",
"\n",
"
"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Before proceeding, let's do a bit of subsetting. Here I want to remove the `Orphan VJ` cells (lacking BCR heavy chain i.e. VDJ information). Whether or not you want to do this is up to you. I'm doing this because I want to focus on the BCR heavy chain for now. You may elect to keep everything and that can be your starting point for further analysis."
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Dandelion class object with n_obs = 2334 and n_contigs = 5557\n",
" data: 'sequence_id', 'sequence', 'rev_comp', 'productive', 'v_call', 'd_call', 'j_call', 'sequence_alignment', 'germline_alignment', 'junction', 'junction_aa', 'v_cigar', 'd_cigar', 'j_cigar', 'stop_codon', 'vj_in_frame', 'locus', 'c_call', 'junction_length', 'np1_length', 'np2_length', 'v_sequence_start', 'v_sequence_end', 'v_germline_start', 'v_germline_end', 'd_sequence_start', 'd_sequence_end', 'd_germline_start', 'd_germline_end', 'j_sequence_start', 'j_sequence_end', 'j_germline_start', 'j_germline_end', 'v_score', 'v_identity', 'v_support', 'd_score', 'd_identity', 'd_support', 'j_score', 'j_identity', 'j_support', 'fwr1', 'fwr2', 'fwr3', 'fwr4', 'cdr1', 'cdr2', 'cdr3', 'cell_id', 'consensus_count', 'umi_count', 'v_call_10x', 'd_call_10x', 'j_call_10x', 'junction_10x', 'junction_10x_aa', 'j_support_igblastn', 'j_score_igblastn', 'j_call_igblastn', 'j_call_blastn', 'j_identity_blastn', 'j_alignment_length_blastn', 'j_number_of_mismatches_blastn', 'j_number_of_gap_openings_blastn', 'j_sequence_start_blastn', 'j_sequence_end_blastn', 'j_germline_start_blastn', 'j_germline_end_blastn', 'j_support_blastn', 'j_score_blastn', 'j_sequence_alignment_blastn', 'j_germline_alignment_blastn', 'j_source', 'd_support_igblastn', 'd_score_igblastn', 'd_call_igblastn', 'd_call_blastn', 'd_identity_blastn', 'd_alignment_length_blastn', 'd_number_of_mismatches_blastn', 'd_number_of_gap_openings_blastn', 'd_sequence_start_blastn', 'd_sequence_end_blastn', 'd_germline_start_blastn', 'd_germline_end_blastn', 'd_support_blastn', 'd_score_blastn', 'd_sequence_alignment_blastn', 'd_germline_alignment_blastn', 'd_source', 'v_call_genotyped', 'germline_alignment_d_mask', 'sample_id', 'c_sequence_alignment', 'c_germline_alignment', 'c_sequence_start', 'c_sequence_end', 'c_score', 'c_identity', 'c_call_10x', 'junction_aa_length', 'fwr1_aa', 'fwr2_aa', 'fwr3_aa', 'fwr4_aa', 'cdr1_aa', 'cdr2_aa', 'cdr3_aa', 'sequence_alignment_aa', 'v_sequence_alignment_aa', 'd_sequence_alignment_aa', 'j_sequence_alignment_aa', 'complete_vdj', 'j_call_multimappers', 'j_call_multiplicity', 'j_call_sequence_start_multimappers', 'j_call_sequence_end_multimappers', 'j_call_support_multimappers', 'mu_count', 'ambiguous', 'extra', 'rearrangement_status', 'clone_id'\n",
" metadata: 'clone_id', 'clone_id_rank', 'sample_id', 'locus_VDJ', 'locus_VJ', 'productive_VDJ', 'productive_VJ', 'v_call_VDJ', 'd_call_VDJ', 'j_call_VDJ', 'v_call_VJ', 'j_call_VJ', 'c_call_VDJ', 'c_call_VJ', 'junction_VDJ', 'junction_VJ', 'junction_aa_VDJ', 'junction_aa_VJ', 'v_call_B_VDJ', 'd_call_B_VDJ', 'j_call_B_VDJ', 'v_call_B_VJ', 'j_call_B_VJ', 'c_call_B_VDJ', 'c_call_B_VJ', 'productive_B_VDJ', 'productive_B_VJ', 'umi_count_B_VDJ', 'umi_count_B_VJ', 'v_call_VDJ_main', 'v_call_VJ_main', 'd_call_VDJ_main', 'j_call_VDJ_main', 'j_call_VJ_main', 'c_call_VDJ_main', 'c_call_VJ_main', 'v_call_B_VDJ_main', 'd_call_B_VDJ_main', 'j_call_B_VDJ_main', 'v_call_B_VJ_main', 'j_call_B_VJ_main', 'isotype', 'isotype_status', 'locus_status', 'chain_status', 'rearrangement_status_VDJ', 'rearrangement_status_VJ'"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"vdj = vdj[\n",
" vdj.metadata.chain_status.isin(\n",
" [\"Single pair\", \"Extra pair\", \"Extra pair-exception\", \"Orphan VDJ\"]\n",
" )\n",
"].copy()\n",
"vdj"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Generating network\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Setting up data: 4877it [00:00, 8253.09it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Calculating distance matrix with distance_mode = 'clone'\n",
"\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 2515/2515 [00:00<00:00, 11254.80it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Distances calculated in 0.23 seconds\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"Sorting into clusters : 100%|██████████| 2515/2515 [00:00<00:00, 5849.10it/s]\n",
"Calculating minimum spanning tree : 100%|██████████| 64/64 [00:00<00:00, 1299.81it/s]\n",
"Generating edge list : 100%|██████████| 64/64 [00:00<00:00, 3674.13it/s]\n",
"Computing overlap : 100%|██████████| 2515/2515 [00:01<00:00, 2383.33it/s]\n",
"Adjust overlap : 100%|██████████| 153/153 [00:00<00:00, 3886.23it/s]\n",
"Linking edges : 100%|██████████| 2252/2252 [00:01<00:00, 1762.20it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Computing network layout\n",
"Computing expanded network layout\n",
" finished.\n",
" Updated Dandelion object\n",
": 'layout', graph layout\n",
" (0:00:18)\n"
]
}
],
"source": [
"ddl.tl.generate_network(vdj)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"At this point, we can save the dandelion object. We will visualise the network in the next tutorial."
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"vdj.write_h5ddl(\"dandelion_results_simplified.h5ddl\", compression=\"gzip\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Full pairwise distance computation\n",
"\n",
"With version 1.0.0, we are bringing back the option to compute the full pairwise distance matrix for every pair of cells. This is useful if you want to have a more comprehensive view of the relationships between cells, rather than just within clones. However, this can be quite memory intensive, especially for large datasets. For that purpose, we have refactored the distance computation to allow for parallelization, as well as with lazy evaluation using `dask` and `zarr` arrays, which allows for handling larger datasets without running into memory issues. While this can also be used for `distance_mode='clone'`, it's incredibly slow. Its main advantage is for `distance_mode='full'` due to contigous nature of the distance matrix.\n",
"\n",
"Note that with `distance_mode='full'`, the required memory scales quadratically with the number of cells, so be cautious when using this option with large datasets. Using `dask` and `zarr` arrays can help mitigate this issue by allowing for out-of-core computation and parallel processing. This will create a `zarr` array on disk to store the distance matrix, which can later be read into memory in the `dandelion` object with `vdj.compute()`, or specifying the path to the `zarr` array when reading the `Dandelion` object with `ddl.read_h5ddl`.\n",
"\n",
"Finally, while pairwise distance computation is now possible, the final graph and layout is still based on within-clone distances only for performance reasons i.e. it will behave as before. In the future, we may explore options to incorporate full pairwise distances into the graph construction and visualization. We will demonstrate alternative ways to visualise the full pairwise distances in a later tutorial where use use `UMAP` and `wnn` on the full distance matrix."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"To be able to use `lazy=True`, you need to have `dask`, `zarr` and `distributed` installed in your environment.\n",
"\n",
"```bash\n",
"pip install \"sc-dandelion[dask]\"\n",
"```\n",
"\n",
"### Caveats with lazy distance matrix computation\n",
"\n",
"With `lazy=True`, the distance matrix computation will be performed lazily on disk, which allows for handling larger datasets without running into memory issues. This is particularly useful when calculating the full pairwise distance matrix for every pair of cells, which can be quite memory-intensive.\n",
"\n",
"While this can also be used for `distance_mode='clone'`, it's incredibly slow. Its main advantage is for `distance_mode='full'` due to contigous nature of the distance matrix.\n",
"\n",
"The `.distances` slot will now contain a `dask` array instead of a compressed sparse matrix. You can compute the distance matrix into memory by calling `vdj.compute()`."
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Generating network\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Setting up data: 4877it [00:00, 8377.85it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Calculating distance matrix lazily with distance_mode = 'full'\n",
"\n",
"Auto computation chunk size: 2334 sequences per block\n",
"Estimated memory per block: 0.04 GB\n",
"Zarr storage chunk size: 2334\n",
"Output size: 0.04 GB uncompressed\n",
"\n",
"Created Zarr array at: distance_matrix.zarr\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/opt/homebrew/Caskroom/miniforge/base/envs/dandelion/lib/python3.12/site-packages/distributed/node.py:188: UserWarning: Port 8787 is already in use.\n",
"Perhaps you already have a cluster running?\n",
"Hosting the HTTP server on port 53308 instead\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Dask client started: http://127.0.0.1:53308/status\n",
"Setting up Dask scheduler and task graph...\n",
"Starting computation of 36 chunks...\n",
"Merging temporary results into final Zarr array...\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 36/36 [00:13<00:00, 2.75it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"============================================================\n",
"\n",
"✓ Distance matrix complete!\n",
"\n",
"Final array info:\n",
" Shape: (2334, 2334)\n",
" Dtype: float64\n",
" Chunks: (2334, 2334)\n",
" Size on disk: 0.04 GB uncompressed\n",
" Actual size: 0.01 GB (with compression)\n",
" Compression ratio: 5.4x\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Sorting into clusters : 100%|██████████| 2515/2515 [03:18<00:00, 12.66it/s]\n",
"Calculating minimum spanning tree : 100%|██████████| 64/64 [00:00<00:00, 1239.04it/s]\n",
"Generating edge list : 100%|██████████| 64/64 [00:00<00:00, 662.53it/s]\n",
"Computing overlap : 100%|██████████| 2515/2515 [00:00<00:00, 2614.68it/s]\n",
"Adjust overlap : 100%|██████████| 153/153 [00:00<00:00, 4197.87it/s]\n",
"Linking edges : 100%|██████████| 2252/2252 [00:01<00:00, 1623.86it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Computing network layout\n",
"Computing expanded network layout\n",
" finished.\n",
" Updated Dandelion object\n",
": 'layout', graph layout\n",
" (0:05:05)\n"
]
}
],
"source": [
"# we will demonstrate one example here where we use the lazy method to compute the network\n",
"vdj_lazy = vdj.copy()\n",
"# unlike the polars version, there's no option to not use existing distances because the base version does not store the precomputed distance during find_clones step.\n",
"ddl.tl.generate_network(\n",
" vdj_lazy,\n",
" use_existing_graph=False,\n",
" distance_mode=\"full\",\n",
" lazy=True,\n",
" n_cpus=8,\n",
" zarr_path=\"distance_matrix.zarr\", # this is where the final computed distance matrix will be stored on disk\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Dandelion class object with n_obs = 2334 and n_contigs = 5557\n",
" data: 'sequence_id', 'sequence', 'rev_comp', 'productive', 'v_call', 'd_call', 'j_call', 'sequence_alignment', 'germline_alignment', 'junction', 'junction_aa', 'v_cigar', 'd_cigar', 'j_cigar', 'stop_codon', 'vj_in_frame', 'locus', 'c_call', 'junction_length', 'np1_length', 'np2_length', 'v_sequence_start', 'v_sequence_end', 'v_germline_start', 'v_germline_end', 'd_sequence_start', 'd_sequence_end', 'd_germline_start', 'd_germline_end', 'j_sequence_start', 'j_sequence_end', 'j_germline_start', 'j_germline_end', 'v_score', 'v_identity', 'v_support', 'd_score', 'd_identity', 'd_support', 'j_score', 'j_identity', 'j_support', 'fwr1', 'fwr2', 'fwr3', 'fwr4', 'cdr1', 'cdr2', 'cdr3', 'cell_id', 'consensus_count', 'umi_count', 'v_call_10x', 'd_call_10x', 'j_call_10x', 'junction_10x', 'junction_10x_aa', 'j_support_igblastn', 'j_score_igblastn', 'j_call_igblastn', 'j_call_blastn', 'j_identity_blastn', 'j_alignment_length_blastn', 'j_number_of_mismatches_blastn', 'j_number_of_gap_openings_blastn', 'j_sequence_start_blastn', 'j_sequence_end_blastn', 'j_germline_start_blastn', 'j_germline_end_blastn', 'j_support_blastn', 'j_score_blastn', 'j_sequence_alignment_blastn', 'j_germline_alignment_blastn', 'j_source', 'd_support_igblastn', 'd_score_igblastn', 'd_call_igblastn', 'd_call_blastn', 'd_identity_blastn', 'd_alignment_length_blastn', 'd_number_of_mismatches_blastn', 'd_number_of_gap_openings_blastn', 'd_sequence_start_blastn', 'd_sequence_end_blastn', 'd_germline_start_blastn', 'd_germline_end_blastn', 'd_support_blastn', 'd_score_blastn', 'd_sequence_alignment_blastn', 'd_germline_alignment_blastn', 'd_source', 'v_call_genotyped', 'germline_alignment_d_mask', 'sample_id', 'c_sequence_alignment', 'c_germline_alignment', 'c_sequence_start', 'c_sequence_end', 'c_score', 'c_identity', 'c_call_10x', 'junction_aa_length', 'fwr1_aa', 'fwr2_aa', 'fwr3_aa', 'fwr4_aa', 'cdr1_aa', 'cdr2_aa', 'cdr3_aa', 'sequence_alignment_aa', 'v_sequence_alignment_aa', 'd_sequence_alignment_aa', 'j_sequence_alignment_aa', 'complete_vdj', 'j_call_multimappers', 'j_call_multiplicity', 'j_call_sequence_start_multimappers', 'j_call_sequence_end_multimappers', 'j_call_support_multimappers', 'mu_count', 'ambiguous', 'extra', 'rearrangement_status', 'clone_id'\n",
" metadata: 'clone_id', 'clone_id_rank', 'sample_id', 'locus_VDJ', 'locus_VJ', 'productive_VDJ', 'productive_VJ', 'v_call_VDJ', 'd_call_VDJ', 'j_call_VDJ', 'v_call_VJ', 'j_call_VJ', 'c_call_VDJ', 'c_call_VJ', 'junction_VDJ', 'junction_VJ', 'junction_aa_VDJ', 'junction_aa_VJ', 'v_call_B_VDJ', 'd_call_B_VDJ', 'j_call_B_VDJ', 'v_call_B_VJ', 'j_call_B_VJ', 'c_call_B_VDJ', 'c_call_B_VJ', 'productive_B_VDJ', 'productive_B_VJ', 'umi_count_B_VDJ', 'umi_count_B_VJ', 'v_call_VDJ_main', 'v_call_VJ_main', 'd_call_VDJ_main', 'j_call_VDJ_main', 'j_call_VJ_main', 'c_call_VDJ_main', 'c_call_VJ_main', 'v_call_B_VDJ_main', 'd_call_B_VDJ_main', 'j_call_B_VDJ_main', 'v_call_B_VJ_main', 'j_call_B_VJ_main', 'isotype', 'isotype_status', 'locus_status', 'chain_status', 'rearrangement_status_VDJ', 'rearrangement_status_VJ'\n",
" layout: layout for 2334 vertices, layout for 146 vertices\n",
" graph: networkx graph of 2334 vertices, networkx graph of 146 vertices \n",
" distances: distance matrix of shape (2334, 2334)"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# view the vdj object\n",
"vdj_lazy"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/uqztuong/Documents/GitHub/dandelion/src/dandelion/base/core/_core.py:1718: FutureWarning: Passing storage-related arguments via **kwargs is deprecated. Please use the 'zarr_store_kwargs' parameter instead. **kwargs will be removed in a future version.\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"WARNING: Distances are a dask array and cannot be stored inline in .h5ddl. Written to dandelion_results_lazy_distance_matrix.zarr. Pass `distance_zarr='dandelion_results_lazy_distance_matrix.zarr'` when reading, or it will be detected automatically.\n"
]
}
],
"source": [
"# save as well\n",
"vdj_lazy.write_h5ddl(\n",
" \"dandelion_results_lazy_distance_matrix.h5ddl\", compression=\"gzip\"\n",
")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Because the distance matrix is lazy, it is not stored in the `h5ddl` file, but rather as the separate zarr array on disk in `zarr_path` with the same prefix. We will show you how to read this:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Dandelion class object with n_obs = 2334 and n_contigs = 5557\n",
" data: 'sequence_id', 'sequence', 'rev_comp', 'productive', 'v_call', 'd_call', 'j_call', 'sequence_alignment', 'germline_alignment', 'junction', 'junction_aa', 'v_cigar', 'd_cigar', 'j_cigar', 'stop_codon', 'vj_in_frame', 'locus', 'c_call', 'junction_length', 'np1_length', 'np2_length', 'v_sequence_start', 'v_sequence_end', 'v_germline_start', 'v_germline_end', 'd_sequence_start', 'd_sequence_end', 'd_germline_start', 'd_germline_end', 'j_sequence_start', 'j_sequence_end', 'j_germline_start', 'j_germline_end', 'v_score', 'v_identity', 'v_support', 'd_score', 'd_identity', 'd_support', 'j_score', 'j_identity', 'j_support', 'fwr1', 'fwr2', 'fwr3', 'fwr4', 'cdr1', 'cdr2', 'cdr3', 'cell_id', 'consensus_count', 'umi_count', 'v_call_10x', 'd_call_10x', 'j_call_10x', 'junction_10x', 'junction_10x_aa', 'j_support_igblastn', 'j_score_igblastn', 'j_call_igblastn', 'j_call_blastn', 'j_identity_blastn', 'j_alignment_length_blastn', 'j_number_of_mismatches_blastn', 'j_number_of_gap_openings_blastn', 'j_sequence_start_blastn', 'j_sequence_end_blastn', 'j_germline_start_blastn', 'j_germline_end_blastn', 'j_support_blastn', 'j_score_blastn', 'j_sequence_alignment_blastn', 'j_germline_alignment_blastn', 'j_source', 'd_support_igblastn', 'd_score_igblastn', 'd_call_igblastn', 'd_call_blastn', 'd_identity_blastn', 'd_alignment_length_blastn', 'd_number_of_mismatches_blastn', 'd_number_of_gap_openings_blastn', 'd_sequence_start_blastn', 'd_sequence_end_blastn', 'd_germline_start_blastn', 'd_germline_end_blastn', 'd_support_blastn', 'd_score_blastn', 'd_sequence_alignment_blastn', 'd_germline_alignment_blastn', 'd_source', 'v_call_genotyped', 'germline_alignment_d_mask', 'sample_id', 'c_sequence_alignment', 'c_germline_alignment', 'c_sequence_start', 'c_sequence_end', 'c_score', 'c_identity', 'c_call_10x', 'junction_aa_length', 'fwr1_aa', 'fwr2_aa', 'fwr3_aa', 'fwr4_aa', 'cdr1_aa', 'cdr2_aa', 'cdr3_aa', 'sequence_alignment_aa', 'v_sequence_alignment_aa', 'd_sequence_alignment_aa', 'j_sequence_alignment_aa', 'complete_vdj', 'j_call_multimappers', 'j_call_multiplicity', 'j_call_sequence_start_multimappers', 'j_call_sequence_end_multimappers', 'j_call_support_multimappers', 'mu_count', 'ambiguous', 'extra', 'rearrangement_status', 'clone_id'\n",
" metadata: 'clone_id', 'clone_id_rank', 'sample_id', 'locus_VDJ', 'locus_VJ', 'productive_VDJ', 'productive_VJ', 'v_call_VDJ', 'd_call_VDJ', 'j_call_VDJ', 'v_call_VJ', 'j_call_VJ', 'c_call_VDJ', 'c_call_VJ', 'junction_VDJ', 'junction_VJ', 'junction_aa_VDJ', 'junction_aa_VJ', 'v_call_B_VDJ', 'd_call_B_VDJ', 'j_call_B_VDJ', 'v_call_B_VJ', 'j_call_B_VJ', 'c_call_B_VDJ', 'c_call_B_VJ', 'productive_B_VDJ', 'productive_B_VJ', 'umi_count_B_VDJ', 'umi_count_B_VJ', 'v_call_VDJ_main', 'v_call_VJ_main', 'd_call_VDJ_main', 'j_call_VDJ_main', 'j_call_VJ_main', 'c_call_VDJ_main', 'c_call_VJ_main', 'v_call_B_VDJ_main', 'd_call_B_VDJ_main', 'j_call_B_VDJ_main', 'v_call_B_VJ_main', 'j_call_B_VJ_main', 'isotype', 'isotype_status', 'locus_status', 'chain_status', 'rearrangement_status_VDJ', 'rearrangement_status_VJ'\n",
" layout: layout for 2334 vertices, layout for 146 vertices\n",
" graph: networkx graph of 2334 vertices, networkx graph of 146 vertices \n",
" distances: distance matrix of shape (2334, 2334)"
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"vdj_lazy_reload = ddl.read_h5ddl(\n",
" \"dandelion_results_lazy_distance_matrix.h5ddl\",\n",
" distance_zarr=\"dandelion_results_lazy_distance_matrix.zarr\",\n",
")\n",
"vdj_lazy_reload"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
" \n",
" \n",
" \n",
" \n",
" \n",
" \n",
" Array \n",
" Chunk \n",
" \n",
" \n",
" \n",
" \n",
" \n",
" Bytes \n",
" 41.56 MiB \n",
" 41.56 MiB \n",
" \n",
" \n",
" \n",
" Shape \n",
" (2334, 2334) \n",
" (2334, 2334) \n",
" \n",
" \n",
" Dask graph \n",
" 1 chunks in 2 graph layers \n",
" \n",
" \n",
" Data type \n",
" float64 numpy.ndarray \n",
" \n",
" \n",
"
\n",
" \n",
" \n",
" \n",
"\n",
" \n",
" \n",
"\n",
" \n",
" 2334 \n",
" 2334 \n",
" \n",
" \n",
" \n",
"
"
],
"text/plain": [
"dask.array"
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"vdj_lazy_reload.distances"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The distance matrix is read lazily as a `dask.array.Array`. To materialize the distance matrix into memory as a CSR sparse matrix, you can call `vdj.compute()`. Note that this will load the entire distance matrix into memory, so make sure you have enough RAM available."
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
""
]
},
"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"vdj_lazy_reload.compute()\n",
"vdj_lazy_reload.distances"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "dandelion",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.9"
}
},
"nbformat": 4,
"nbformat_minor": 4
}