{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Interoperability with `scirpy`\n", "\n", "It is now possible to convert the file formats between `dandelion>=0.1.1` and `scirpy>=0.6.2` [[Sturm2020]](https://academic.oup.com/bioinformatics/article/36/18/4817/5866543) to enhance the collaboration between the analysis toolkits.\n", "\n", "We will download the *airr_rearrangement.tsv* file from here:\n", "```bash\n", "# bash\n", "wget https://cf.10xgenomics.com/samples/cell-vdj/4.0.0/sc5p_v2_hs_PBMC_10k/sc5p_v2_hs_PBMC_10k_b_airr_rearrangement.tsv\n", "```\n", "\n", "Gene expression data can also be obtained here\n", "\n", "```bash\n", "# bash \n", "wget https://cf.10xgenomics.com/samples/cell-vdj/4.0.0/sc5p_v2_hs_PBMC_10k/sc5p_v2_hs_PBMC_10k_filtered_feature_bc_matrix.h5\n", "```\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Import dandelion module" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "dandelion==0.5.5.dev16 pandas==2.2.3 numpy==2.1.3 matplotlib==3.10.1 networkx==3.4.2 scipy==1.15.2\n" ] } ], "source": [ "# import sys\n", "# sys.path.append(\"C://Users//Amos Choo//Desktop//dandelion\")\n", "import os\n", "\n", "import dandelion as ddl\n", "\n", "\n", "# change directory to somewhere more workable\n", "\n", "os.chdir(os.path.expanduser(\"~/Downloads/dandelion_tutorial/\"))\n", "\n", "ddl.logging.print_versions()" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "'0.22.1.dev1+gb32fd24'" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import scirpy as ir\n", "import scanpy as sc\n", "\n", "\n", "ir.__version__" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## `dandelion`" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "scrolled": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/opt/homebrew/Caskroom/miniforge/base/envs/dandelion/lib/python3.11/site-packages/anndata/_core/anndata.py:1758: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n", "/opt/homebrew/Caskroom/miniforge/base/envs/dandelion/lib/python3.11/site-packages/anndata/_core/anndata.py:1758: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n" ] }, { "data": { "text/plain": [ "Dandelion class object with n_obs = 5351 and n_contigs = 10860\n", " data: 'cell_id', 'sequence_id', 'sequence', 'sequence_aa', 'productive', 'rev_comp', 'v_call', 'v_cigar', 'd_call', 'd_cigar', 'j_call', 'j_cigar', 'c_call', 'c_cigar', 'sequence_alignment', 'germline_alignment', 'junction', 'junction_aa', 'junction_length', 'junction_aa_length', 'v_sequence_start', 'v_sequence_end', 'd_sequence_start', 'd_sequence_end', 'j_sequence_start', 'j_sequence_end', 'c_sequence_start', 'c_sequence_end', 'consensus_count', 'umi_count', 'is_cell', 'locus', 'rearrangement_status'\n", " metadata: '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_abT_VDJ', 'd_call_abT_VDJ', 'j_call_abT_VDJ', 'v_call_abT_VJ', 'j_call_abT_VJ', 'c_call_abT_VDJ', 'c_call_abT_VJ', 'productive_abT_VDJ', 'productive_abT_VJ', 'umi_count_abT_VDJ', 'umi_count_abT_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_abT_VDJ_main', 'd_call_abT_VDJ_main', 'j_call_abT_VDJ_main', 'v_call_abT_VJ_main', 'j_call_abT_VJ_main', 'isotype', 'isotype_status', 'locus_status', 'chain_status', 'rearrangement_status_VDJ', 'rearrangement_status_VJ'" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# read in the airr_rearrangement.tsv file\n", "file_location = (\n", " \"sc5p_v2_hs_PBMC_10k/sc5p_v2_hs_PBMC_10k_t_airr_rearrangement.tsv\"\n", ")\n", "\n", "# read in gene expression data\n", "adata = sc.read_10x_h5(\n", " \"sc5p_v2_hs_PBMC_10k/sc5p_v2_hs_PBMC_10k_filtered_feature_bc_matrix.h5\"\n", ")\n", "adata.var_names_make_unique()\n", "\n", "vdj = ddl.read_10x_airr(file_location)\n", "vdj" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The test file contains a blank `clone_id` column so we run `find_clones` to populate it first." ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Finding clones based on abT cell VDJ chains : 100%|██████████| 512/512 [00:00<00:00, 1157.38it/s]\n", "Finding clones based on abT cell VJ chains : 100%|██████████| 1574/1574 [00:00<00:00, 10558.22it/s]\n", "Refining clone assignment based on VJ chain pairing : 100%|██████████| 5351/5351 [00:00<00:00, 230665.17it/s]\n" ] } ], "source": [ "ddl.tl.find_clones(vdj)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### `ddl.to_scirpy` : Converting `dandelion` to `scirpy`" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "scrolled": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/opt/homebrew/Caskroom/miniforge/base/envs/dandelion/lib/python3.11/site-packages/anndata/utils.py:349: ExperimentalFeatureWarning: Support for Awkward Arrays is currently experimental. Behavior may change in the future. Please report any issues you may encounter!\n", "/opt/homebrew/Caskroom/miniforge/base/envs/dandelion/lib/python3.11/site-packages/mudata/_core/mudata.py:1531: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.\n", "/opt/homebrew/Caskroom/miniforge/base/envs/dandelion/lib/python3.11/site-packages/mudata/_core/mudata.py:1429: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.\n" ] }, { "data": { "text/html": [ "
MuData object with n_obs × n_vars = 5351 × 0\n",
" 1 modality\n",
" airr:\t5351 x 0\n",
" obsm:\t'airr'"
],
"text/plain": [
"MuData object with n_obs × n_vars = 5351 × 0\n",
" 1 modality\n",
" airr:\t5351 x 0\n",
" obsm:\t'airr'"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"irdata = ddl.to_scirpy(vdj)\n",
"irdata"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Conversion to `AnndData` in scirpy format is also available"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"AnnData object with n_obs × n_vars = 5351 × 0\n",
" obsm: 'airr'"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mudata = ddl.to_scirpy(vdj, to_mudata=False)\n",
"mudata"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If you have gene expression data, the parameter `gex_adata` supports the gene expression data in `AnnData` format.\n",
"\n",
"Please note that this will slice to the same cell_id that are present in the same in the AIRR data."
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"AnnData object with n_obs × n_vars = 5333 × 36601\n",
" var: 'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'\n",
" obsm: 'airr'"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"irdata = ddl.to_scirpy(vdj, to_mudata=False, gex_adata=adata)\n",
"irdata"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/opt/homebrew/Caskroom/miniforge/base/envs/dandelion/lib/python3.11/site-packages/mudata/_core/mudata.py:1531: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.\n",
"/opt/homebrew/Caskroom/miniforge/base/envs/dandelion/lib/python3.11/site-packages/mudata/_core/mudata.py:1429: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.\n"
]
},
{
"data": {
"text/html": [
"MuData object with n_obs × n_vars = 10571 × 36601\n",
" 2 modalities\n",
" gex:\t10553 x 36601\n",
" var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'\n",
" airr:\t5351 x 0\n",
" obsm:\t'airr'"
],
"text/plain": [
"MuData object with n_obs × n_vars = 10571 × 36601\n",
" 2 modalities\n",
" gex:\t10553 x 36601\n",
" var:\t'gene_ids', 'feature_types', 'genome', 'pattern', 'read', 'sequence'\n",
" airr:\t5351 x 0\n",
" obsm:\t'airr'"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mudata = ddl.to_scirpy(vdj, to_mudata=True, gex_adata=adata)\n",
"mudata"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Use scirpy's get functions to retrieve the relevant airr info (https://scirpy.scverse.org/en/latest/generated/scirpy.get.airr.html)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"WARNING: No chain indices found under adata.obsm['chain_indices']. Running scirpy.pp.index_chains with default parameters. \n"
]
},
{
"data": {
"application/vnd.microsoft.datawrangler.viewer.v0+json": {
"columns": [
{
"name": "index",
"rawType": "object",
"type": "string"
},
{
"name": "VJ_1_clone_id",
"rawType": "object",
"type": "unknown"
},
{
"name": "VDJ_1_clone_id",
"rawType": "object",
"type": "unknown"
},
{
"name": "VJ_2_clone_id",
"rawType": "object",
"type": "unknown"
},
{
"name": "VDJ_2_clone_id",
"rawType": "object",
"type": "unknown"
}
],
"conversionMethod": "pd.DataFrame",
"ref": "3a8d6b19-6a57-437a-9a3a-5a1f04eb2bdb",
"rows": [
[
"AAACCTGAGCGATAGC-1",
"abT_VDJ_119_5_2_VJ_306_2_3",
"abT_VDJ_119_5_2_VJ_306_2_3",
null,
null
],
[
"AAACCTGAGTCACGCC-1",
"abT_VDJ_225_5_1_VJ_1416_1_1",
"abT_VDJ_225_5_1_VJ_1416_1_1",
null,
null
],
[
"AAACCTGCACGTCAGC-1",
"abT_VDJ_225_2_1_VJ_211_2_8",
"abT_VDJ_225_2_1_VJ_211_2_8",
null,
null
],
[
"AAACCTGGTCAATACC-1",
"abT_VDJ_282_4_3_VJ_1376_2_1",
"abT_VDJ_282_4_3_VJ_1376_2_1",
null,
null
],
[
"AAACCTGGTTCGGCAC-1",
"abT_VDJ_214_4_8_VJ_1536_2_1|abT_VDJ_214_4_8_VJ_1113_2_1",
"abT_VDJ_214_4_8_VJ_1536_2_1|abT_VDJ_214_4_8_VJ_1113_2_1",
"abT_VDJ_214_4_8_VJ_1536_2_1|abT_VDJ_214_4_8_VJ_1113_2_1",
null
],
[
"AAACCTGGTTGAACTC-1",
"abT_VDJ_511_2_1_VJ_863_1_1",
"abT_VDJ_511_2_1_VJ_863_1_1",
null,
null
],
[
"AAACCTGTCACGACTA-1",
"abT_VDJ_25_2_2_VJ_919_1_1",
"abT_VDJ_25_2_2_VJ_919_1_1",
null,
null
],
[
"AAACCTGTCCGAGCCA-1",
null,
"abT_VDJ_445_3_4",
null,
null
],
[
"AAACCTGTCGTCTGAA-1",
"abT_VDJ_148_4_1_VJ_1329_1_1",
"abT_VDJ_148_4_1_VJ_1329_1_1",
null,
null
],
[
"AAACCTGTCTTACCGC-1",
"abT_VJ_1092_4_2",
null,
null,
null
],
[
"AAACCTGTCTTGACGA-1",
"abT_VDJ_500_1_2_VJ_856_2_1",
"abT_VDJ_500_1_2_VJ_856_2_1",
null,
null
],
[
"AAACGGGAGACCCACC-1",
"abT_VDJ_28_4_5_VJ_1198_4_2",
"abT_VDJ_28_4_5_VJ_1198_4_2",
null,
null
],
[
"AAACGGGAGGATGTAT-1",
"abT_VDJ_80_6_5_VJ_1337_2_1",
"abT_VDJ_80_6_5_VJ_1337_2_1",
null,
null
],
[
"AAACGGGAGTGTTTGC-1",
"abT_VDJ_400_7_2_VJ_1411_1_1",
"abT_VDJ_400_7_2_VJ_1411_1_1",
null,
null
],
[
"AAACGGGGTAAACGCG-1",
"abT_VDJ_188_2_3_VJ_381_1_1",
"abT_VDJ_188_2_3_VJ_381_1_1",
null,
null
],
[
"AAACGGGGTAGCCTCG-1",
"abT_VJ_1180_4_5",
null,
null,
null
],
[
"AAACGGGTCACGATGT-1",
"abT_VDJ_509_8_1_VJ_1086_2_2",
"abT_VDJ_509_8_1_VJ_1086_2_2",
null,
null
],
[
"AAACGGGTCAGGTAAA-1",
"abT_VDJ_393_8_1_VJ_553_1_1",
"abT_VDJ_393_8_1_VJ_553_1_1",
null,
null
],
[
"AAACGGGTCCGCGCAA-1",
"abT_VDJ_327_4_4_VJ_1263_1_1",
"abT_VDJ_327_4_4_VJ_1263_1_1",
null,
null
],
[
"AAACGGGTCGGATGTT-1",
"abT_VDJ_429_1_1_VJ_1115_2_1",
"abT_VDJ_429_1_1_VJ_1115_2_1",
null,
null
],
[
"AAACGGGTCTAACGGT-1",
"abT_VDJ_62_2_1_VJ_1573_1_1",
"abT_VDJ_62_2_1_VJ_1573_1_1",
null,
null
],
[
"AAAGATGAGCAGACTG-1",
"abT_VDJ_359_1_7_VJ_1105_1_1",
"abT_VDJ_359_1_7_VJ_1105_1_1",
null,
null
],
[
"AAAGATGAGGTGCAAC-1",
"abT_VDJ_212_4_3_VJ_717_5_1",
"abT_VDJ_212_4_3_VJ_717_5_1",
null,
null
],
[
"AAAGATGAGTGGGATC-1",
"abT_VDJ_194_6_1_VJ_1279_4_3",
"abT_VDJ_194_6_1_VJ_1279_4_3",
null,
null
],
[
"AAAGATGCATCTCGCT-1",
"abT_VDJ_412_6_3_VJ_361_2_1",
"abT_VDJ_412_6_3_VJ_361_2_1",
null,
null
],
[
"AAAGATGGTACTTCTT-1",
"abT_VDJ_421_3_1_VJ_203_3_1",
"abT_VDJ_421_3_1_VJ_203_3_1",
null,
null
],
[
"AAAGATGGTCCCTTGT-1",
"abT_VDJ_43_5_1_VJ_248_3_3",
"abT_VDJ_43_5_1_VJ_248_3_3",
null,
null
],
[
"AAAGATGTCGGAATCT-1",
"abT_VDJ_292_2_1_VJ_550_1_1|abT_VDJ_292_2_1_VJ_1385_2_1",
"abT_VDJ_292_2_1_VJ_550_1_1|abT_VDJ_292_2_1_VJ_1385_2_1",
"abT_VDJ_292_2_1_VJ_550_1_1|abT_VDJ_292_2_1_VJ_1385_2_1",
null
],
[
"AAAGATGTCTGTCTCG-1",
"abT_VDJ_260_3_2_VJ_818_1_1",
"abT_VDJ_260_3_2_VJ_818_1_1",
null,
null
],
[
"AAAGCAAAGAGGGATA-1",
"abT_VDJ_57_3_1_VJ_867_2_1",
"abT_VDJ_57_3_1_VJ_867_2_1",
null,
null
],
[
"AAAGCAAAGTAGGCCA-1",
"abT_VDJ_255_3_2_VJ_1182_1_3",
"abT_VDJ_255_3_2_VJ_1182_1_3",
null,
null
],
[
"AAAGCAAAGTGCAAGC-1",
"abT_VDJ_139_4_4_VJ_1481_2_1",
"abT_VDJ_139_4_4_VJ_1481_2_1",
null,
null
],
[
"AAAGCAAGTAAACACA-1",
"abT_VDJ_496_4_1_VJ_706_3_1",
"abT_VDJ_496_4_1_VJ_706_3_1",
null,
null
],
[
"AAAGCAAGTTCAACCA-1",
"abT_VDJ_345_4_6_VJ_1350_1_1",
"abT_VDJ_345_4_6_VJ_1350_1_1",
null,
null
],
[
"AAAGCAAGTTCAGGCC-1",
"abT_VDJ_296_1_1_VJ_525_1_1",
"abT_VDJ_296_1_1_VJ_525_1_1",
null,
null
],
[
"AAAGCAAGTTTACTCT-1",
"abT_VDJ_163_3_1_VJ_125_3_1|abT_VDJ_311_4_6_VJ_125_3_1",
"abT_VDJ_163_3_1_VJ_125_3_1|abT_VDJ_311_4_6_VJ_125_3_1",
null,
"abT_VDJ_163_3_1_VJ_125_3_1|abT_VDJ_311_4_6_VJ_125_3_1"
],
[
"AAAGCAATCAGTTCGA-1",
"abT_VDJ_119_5_6_VJ_319_3_1|abT_VDJ_119_5_6_VJ_43_3_1",
"abT_VDJ_119_5_6_VJ_319_3_1|abT_VDJ_119_5_6_VJ_43_3_1",
"abT_VDJ_119_5_6_VJ_319_3_1|abT_VDJ_119_5_6_VJ_43_3_1",
null
],
[
"AAAGCAATCATATCGG-1",
"abT_VDJ_22_1_2_VJ_1505_4_1",
"abT_VDJ_22_1_2_VJ_1505_4_1",
null,
null
],
[
"AAAGCAATCTGAGTGT-1",
"abT_VDJ_409_8_1_VJ_373_4_2",
"abT_VDJ_409_8_1_VJ_373_4_2",
null,
null
],
[
"AAAGTAGAGCCAGTAG-1",
"abT_VDJ_45_1_1_VJ_1123_1_2|abT_VDJ_45_1_1_VJ_451_1_1",
"abT_VDJ_45_1_1_VJ_1123_1_2|abT_VDJ_45_1_1_VJ_451_1_1",
"abT_VDJ_45_1_1_VJ_1123_1_2|abT_VDJ_45_1_1_VJ_451_1_1",
null
],
[
"AAAGTAGCAAGGCTCC-1",
"abT_VDJ_87_2_2_VJ_1049_1_1|abT_VDJ_87_2_2_VJ_640_2_2",
"abT_VDJ_87_2_2_VJ_1049_1_1|abT_VDJ_87_2_2_VJ_640_2_2",
"abT_VDJ_87_2_2_VJ_1049_1_1|abT_VDJ_87_2_2_VJ_640_2_2",
null
],
[
"AAAGTAGCAATGGTCT-1",
"abT_VDJ_405_3_2_VJ_341_4_1",
"abT_VDJ_405_3_2_VJ_341_4_1",
null,
null
],
[
"AAAGTAGCAGCTGCAC-1",
"abT_VDJ_307_3_3_VJ_136_1_2",
"abT_VDJ_307_3_3_VJ_136_1_2",
null,
null
],
[
"AAAGTAGGTACCAGTT-1",
"abT_VDJ_214_4_7_VJ_1533_1_1",
"abT_VDJ_214_4_7_VJ_1533_1_1",
null,
null
],
[
"AAAGTAGGTCATACTG-1",
"abT_VDJ_134_1_2_VJ_491_2_1",
"abT_VDJ_134_1_2_VJ_491_2_1",
null,
null
],
[
"AAAGTAGGTCCGAACC-1",
"abT_VDJ_142_1_1_VJ_1367_2_1",
"abT_VDJ_142_1_1_VJ_1367_2_1",
null,
null
],
[
"AAAGTAGGTCTGCCAG-1",
"abT_VDJ_501_2_1_VJ_688_1_1",
"abT_VDJ_501_2_1_VJ_688_1_1",
null,
null
],
[
"AAAGTAGGTTCAGGCC-1",
"abT_VDJ_63_2_3_VJ_444_1_1",
"abT_VDJ_63_2_3_VJ_444_1_1",
null,
null
],
[
"AAAGTAGTCAGGCAAG-1",
"abT_VDJ_454_2_1_VJ_271_1_1",
"abT_VDJ_454_2_1_VJ_271_1_1",
null,
null
],
[
"AAAGTAGTCGCATGGC-1",
"abT_VDJ_242_3_3_VJ_1311_1_2",
"abT_VDJ_242_3_3_VJ_1311_1_2",
null,
null
]
],
"shape": {
"columns": 4,
"rows": 5333
}
},
"text/html": [
"| \n", " | VJ_1_clone_id | \n", "VDJ_1_clone_id | \n", "VJ_2_clone_id | \n", "VDJ_2_clone_id | \n", "
|---|---|---|---|---|
| AAACCTGAGCGATAGC-1 | \n", "abT_VDJ_119_5_2_VJ_306_2_3 | \n", "abT_VDJ_119_5_2_VJ_306_2_3 | \n", "None | \n", "None | \n", "
| AAACCTGAGTCACGCC-1 | \n", "abT_VDJ_225_5_1_VJ_1416_1_1 | \n", "abT_VDJ_225_5_1_VJ_1416_1_1 | \n", "None | \n", "None | \n", "
| AAACCTGCACGTCAGC-1 | \n", "abT_VDJ_225_2_1_VJ_211_2_8 | \n", "abT_VDJ_225_2_1_VJ_211_2_8 | \n", "None | \n", "None | \n", "
| AAACCTGGTCAATACC-1 | \n", "abT_VDJ_282_4_3_VJ_1376_2_1 | \n", "abT_VDJ_282_4_3_VJ_1376_2_1 | \n", "None | \n", "None | \n", "
| AAACCTGGTTCGGCAC-1 | \n", "abT_VDJ_214_4_8_VJ_1536_2_1|abT_VDJ_214_4_8_VJ... | \n", "abT_VDJ_214_4_8_VJ_1536_2_1|abT_VDJ_214_4_8_VJ... | \n", "abT_VDJ_214_4_8_VJ_1536_2_1|abT_VDJ_214_4_8_VJ... | \n", "None | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| TTTGTCATCGCCGTGA-1 | \n", "abT_VDJ_382_1_1_VJ_723_1_1 | \n", "abT_VDJ_382_1_1_VJ_723_1_1 | \n", "None | \n", "None | \n", "
| TTTGTCATCGTCTGAA-1 | \n", "abT_VDJ_338_3_1_VJ_592_2_1 | \n", "abT_VDJ_338_3_1_VJ_592_2_1 | \n", "None | \n", "None | \n", "
| TTTGTCATCTACCAGA-1 | \n", "abT_VDJ_502_3_1_VJ_621_3_1 | \n", "abT_VDJ_502_3_1_VJ_621_3_1 | \n", "None | \n", "None | \n", "
| TTTGTCATCTCTGAGA-1 | \n", "abT_VDJ_372_5_1_VJ_1420_1_1|abT_VDJ_58_3_1_VJ_... | \n", "abT_VDJ_372_5_1_VJ_1420_1_1|abT_VDJ_58_3_1_VJ_... | \n", "None | \n", "abT_VDJ_372_5_1_VJ_1420_1_1|abT_VDJ_58_3_1_VJ_... | \n", "
| TTTGTCATCTTCGAGA-1 | \n", "abT_VDJ_359_1_5_VJ_1561_4_1 | \n", "abT_VDJ_359_1_5_VJ_1561_4_1 | \n", "None | \n", "None | \n", "
5333 rows × 4 columns
\n", "| \n", " | VJ_1_clone_id | \n", "VDJ_1_clone_id | \n", "VJ_2_clone_id | \n", "VDJ_2_clone_id | \n", "
|---|---|---|---|---|
| cell_id | \n", "\n", " | \n", " | \n", " | \n", " |
| AAACCTGAGCGATAGC-1 | \n", "abT_VDJ_119_5_2_VJ_306_2_3 | \n", "abT_VDJ_119_5_2_VJ_306_2_3 | \n", "None | \n", "None | \n", "
| AAACCTGAGTCACGCC-1 | \n", "abT_VDJ_225_5_1_VJ_1416_1_1 | \n", "abT_VDJ_225_5_1_VJ_1416_1_1 | \n", "None | \n", "None | \n", "
| AAACCTGCACGTCAGC-1 | \n", "abT_VDJ_225_2_1_VJ_211_2_8 | \n", "abT_VDJ_225_2_1_VJ_211_2_8 | \n", "None | \n", "None | \n", "
| AAACCTGGTCAATACC-1 | \n", "abT_VDJ_282_4_3_VJ_1376_2_1 | \n", "abT_VDJ_282_4_3_VJ_1376_2_1 | \n", "None | \n", "None | \n", "
| AAACCTGGTTCGGCAC-1 | \n", "abT_VDJ_214_4_8_VJ_1536_2_1|abT_VDJ_214_4_8_VJ... | \n", "abT_VDJ_214_4_8_VJ_1536_2_1|abT_VDJ_214_4_8_VJ... | \n", "abT_VDJ_214_4_8_VJ_1536_2_1|abT_VDJ_214_4_8_VJ... | \n", "None | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| TTTGTCATCGCCGTGA-1 | \n", "abT_VDJ_382_1_1_VJ_723_1_1 | \n", "abT_VDJ_382_1_1_VJ_723_1_1 | \n", "None | \n", "None | \n", "
| TTTGTCATCGTCTGAA-1 | \n", "abT_VDJ_338_3_1_VJ_592_2_1 | \n", "abT_VDJ_338_3_1_VJ_592_2_1 | \n", "None | \n", "None | \n", "
| TTTGTCATCTACCAGA-1 | \n", "abT_VDJ_502_3_1_VJ_621_3_1 | \n", "abT_VDJ_502_3_1_VJ_621_3_1 | \n", "None | \n", "None | \n", "
| TTTGTCATCTCTGAGA-1 | \n", "abT_VDJ_372_5_1_VJ_1420_1_1|abT_VDJ_58_3_1_VJ_... | \n", "abT_VDJ_372_5_1_VJ_1420_1_1|abT_VDJ_58_3_1_VJ_... | \n", "None | \n", "abT_VDJ_372_5_1_VJ_1420_1_1|abT_VDJ_58_3_1_VJ_... | \n", "
| TTTGTCATCTTCGAGA-1 | \n", "abT_VDJ_359_1_5_VJ_1561_4_1 | \n", "abT_VDJ_359_1_5_VJ_1561_4_1 | \n", "None | \n", "None | \n", "
5351 rows × 4 columns
\n", "MuData object with n_obs × n_vars = 5351 × 0\n",
" 1 modality\n",
" airr:\t5351 x 0\n",
" obs:\t'clone_id', 'clone_id_by_size', '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_abT_VDJ', 'd_call_abT_VDJ', 'j_call_abT_VDJ', 'v_call_abT_VJ', 'j_call_abT_VJ', 'c_call_abT_VDJ', 'c_call_abT_VJ', 'productive_abT_VDJ', 'productive_abT_VJ', 'umi_count_abT_VDJ', 'umi_count_abT_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_abT_VDJ_main', 'd_call_abT_VDJ_main', 'j_call_abT_VDJ_main', 'v_call_abT_VJ_main', 'j_call_abT_VJ_main', 'isotype', 'isotype_status', 'locus_status', 'chain_status', 'rearrangement_status_VDJ', 'rearrangement_status_VJ'\n",
" obsm:\t'airr'"
],
"text/plain": [
"MuData object with n_obs × n_vars = 5351 × 0\n",
" 1 modality\n",
" airr:\t5351 x 0\n",
" obs:\t'clone_id', 'clone_id_by_size', '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_abT_VDJ', 'd_call_abT_VDJ', 'j_call_abT_VDJ', 'v_call_abT_VJ', 'j_call_abT_VJ', 'c_call_abT_VDJ', 'c_call_abT_VJ', 'productive_abT_VDJ', 'productive_abT_VJ', 'umi_count_abT_VDJ', 'umi_count_abT_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_abT_VDJ_main', 'd_call_abT_VDJ_main', 'j_call_abT_VDJ_main', 'v_call_abT_VJ_main', 'j_call_abT_VJ_main', 'isotype', 'isotype_status', 'locus_status', 'chain_status', 'rearrangement_status_VDJ', 'rearrangement_status_VJ'\n",
" obsm:\t'airr'"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"irdatax = ddl.to_scirpy(vdj, transfer=True)\n",
"irdatax"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"AnnData object with n_obs × n_vars = 5351 × 0\n",
" obs: 'clone_id', 'clone_id_by_size', '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_abT_VDJ', 'd_call_abT_VDJ', 'j_call_abT_VDJ', 'v_call_abT_VJ', 'j_call_abT_VJ', 'c_call_abT_VDJ', 'c_call_abT_VJ', 'productive_abT_VDJ', 'productive_abT_VJ', 'umi_count_abT_VDJ', 'umi_count_abT_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_abT_VDJ_main', 'd_call_abT_VDJ_main', 'j_call_abT_VDJ_main', 'v_call_abT_VJ_main', 'j_call_abT_VJ_main', 'isotype', 'isotype_status', 'locus_status', 'chain_status', 'rearrangement_status_VDJ', 'rearrangement_status_VJ'\n",
" obsm: 'airr'"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"irdatax = ddl.to_scirpy(vdj, transfer=True, to_mudata=False)\n",
"irdatax"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### `ddl.from_scirpy` : Converting `scirpy` to `dandelion`"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Converting `MuData` back to `Dandelion`"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Dandelion class object with n_obs = 5351 and n_contigs = 10860\n",
" data: 'c_call', 'c_cigar', 'c_sequence_end', 'c_sequence_start', 'clone_id', 'consensus_count', 'd_call', 'd_cigar', 'd_sequence_end', 'd_sequence_start', 'germline_alignment', 'is_cell', 'j_call', 'j_cigar', 'j_sequence_end', 'j_sequence_start', 'junction', 'junction_aa', 'junction_aa_length', 'junction_length', 'locus', 'productive', 'rearrangement_status', 'rev_comp', 'sequence', 'sequence_aa', 'sequence_alignment', 'sequence_id', 'umi_count', 'v_call', 'v_cigar', 'v_sequence_end', 'v_sequence_start', 'cell_id'\n",
" metadata: 'clone_id', 'clone_id_by_size', '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_abT_VDJ', 'd_call_abT_VDJ', 'j_call_abT_VDJ', 'v_call_abT_VJ', 'j_call_abT_VJ', 'c_call_abT_VDJ', 'c_call_abT_VJ', 'productive_abT_VDJ', 'productive_abT_VJ', 'umi_count_abT_VDJ', 'umi_count_abT_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_abT_VDJ_main', 'd_call_abT_VDJ_main', 'j_call_abT_VDJ_main', 'v_call_abT_VJ_main', 'j_call_abT_VJ_main', 'isotype', 'isotype_status', 'locus_status', 'chain_status', 'rearrangement_status_VDJ', 'rearrangement_status_VJ'"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"vdjx = ddl.from_scirpy(mudata)\n",
"vdjx"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Converting `AnnData` back to `Dandelion`"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Dandelion class object with n_obs = 5333 and n_contigs = 10836\n",
" data: 'c_call', 'c_cigar', 'c_sequence_end', 'c_sequence_start', 'clone_id', 'consensus_count', 'd_call', 'd_cigar', 'd_sequence_end', 'd_sequence_start', 'germline_alignment', 'is_cell', 'j_call', 'j_cigar', 'j_sequence_end', 'j_sequence_start', 'junction', 'junction_aa', 'junction_aa_length', 'junction_length', 'locus', 'productive', 'rearrangement_status', 'rev_comp', 'sequence', 'sequence_aa', 'sequence_alignment', 'sequence_id', 'umi_count', 'v_call', 'v_cigar', 'v_sequence_end', 'v_sequence_start', 'cell_id'\n",
" metadata: 'clone_id', 'clone_id_by_size', '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_abT_VDJ', 'd_call_abT_VDJ', 'j_call_abT_VDJ', 'v_call_abT_VJ', 'j_call_abT_VJ', 'c_call_abT_VDJ', 'c_call_abT_VJ', 'productive_abT_VDJ', 'productive_abT_VJ', 'umi_count_abT_VDJ', 'umi_count_abT_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_abT_VDJ_main', 'd_call_abT_VDJ_main', 'j_call_abT_VDJ_main', 'v_call_abT_VJ_main', 'j_call_abT_VJ_main', 'isotype', 'isotype_status', 'locus_status', 'chain_status', 'rearrangement_status_VDJ', 'rearrangement_status_VJ'"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"vdjx = ddl.from_scirpy(irdata)\n",
"vdjx"
]
},
{
"cell_type": "code",
"execution_count": 16,
"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_by_size",
"rawType": "category",
"type": "unknown"
},
{
"name": "locus_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "locus_VJ",
"rawType": "object",
"type": "string"
},
{
"name": "productive_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "productive_VJ",
"rawType": "object",
"type": "string"
},
{
"name": "v_call_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "d_call_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "j_call_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "v_call_VJ",
"rawType": "object",
"type": "string"
},
{
"name": "j_call_VJ",
"rawType": "object",
"type": "string"
},
{
"name": "c_call_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "c_call_VJ",
"rawType": "object",
"type": "string"
},
{
"name": "junction_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "junction_VJ",
"rawType": "object",
"type": "string"
},
{
"name": "junction_aa_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "junction_aa_VJ",
"rawType": "object",
"type": "string"
},
{
"name": "v_call_abT_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "d_call_abT_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "j_call_abT_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "v_call_abT_VJ",
"rawType": "object",
"type": "string"
},
{
"name": "j_call_abT_VJ",
"rawType": "object",
"type": "string"
},
{
"name": "c_call_abT_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "c_call_abT_VJ",
"rawType": "object",
"type": "string"
},
{
"name": "productive_abT_VDJ",
"rawType": "object",
"type": "string"
},
{
"name": "productive_abT_VJ",
"rawType": "object",
"type": "string"
},
{
"name": "umi_count_abT_VDJ",
"rawType": "float64",
"type": "float"
},
{
"name": "umi_count_abT_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_abT_VDJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "d_call_abT_VDJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "j_call_abT_VDJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "v_call_abT_VJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "j_call_abT_VJ_main",
"rawType": "object",
"type": "string"
},
{
"name": "isotype",
"rawType": "object",
"type": "string"
},
{
"name": "isotype_status",
"rawType": "object",
"type": "string"
},
{
"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"
}
],
"conversionMethod": "pd.DataFrame",
"ref": "51c0c089-7e4c-4ac9-9130-11e1bd481915",
"rows": [
[
"AAACCTGAGCGATAGC-1",
"abT_VDJ_119_5_2_VJ_306_2_3",
"422",
"TRB",
"TRA",
"True",
"True",
"TRBV6-5",
"None",
"TRBJ2-3",
"TRAV23/DV6",
"TRAJ22",
"TRBC2",
"TRAC",
"TGTGCCAGCAGTTACCGGGGGGGATCGGAAGATACGCAGTATTTT",
"TGTGCAGCAAGCAAGGGTTCTGCAAGGCAACTGACCTTT",
"CASSYRGGSEDTQYF",
"CAASKGSARQLTF",
"TRBV6-5",
"None",
"TRBJ2-3",
"TRAV23/DV6",
"TRAJ22",
"TRBC2",
"TRAC",
"True",
"True",
"9.0",
"11.0",
"TRBV6-5",
"TRAV23/DV6",
"None",
"TRBJ2-3",
"TRAJ22",
"TRBC2",
"TRAC",
"TRBV6-5",
"None",
"TRBJ2-3",
"TRAV23/DV6",
"TRAJ22",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACCTGAGTCACGCC-1",
"abT_VDJ_225_5_1_VJ_1416_1_1",
"5053",
"TRB",
"TRA",
"True",
"True",
"TRBV6-2",
"None",
"TRBJ2-6",
"TRAV8-6",
"TRAJ8",
"TRBC2",
"TRAC",
"TGTGCCAGCAGTTATCTCCCCCGTAGACAGGACAGGGAATCCTCTGGGGCCAACGTCCTGACTTTC",
"TGTGCTGTGAGTGCGTTTTTTCAGAAACTTGTATTT",
"CASSYLPRRQDRESSGANVLTF",
"CAVSAFFQKLVF",
"TRBV6-2",
"None",
"TRBJ2-6",
"TRAV8-6",
"TRAJ8",
"TRBC2",
"TRAC",
"True",
"True",
"12.0",
"9.0",
"TRBV6-2",
"TRAV8-6",
"None",
"TRBJ2-6",
"TRAJ8",
"TRBC2",
"TRAC",
"TRBV6-2",
"None",
"TRBJ2-6",
"TRAV8-6",
"TRAJ8",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACCTGCACGTCAGC-1",
"abT_VDJ_225_2_1_VJ_211_2_8",
"4081",
"TRB",
"TRA",
"True",
"True",
"TRBV6-2",
"None",
"TRBJ2-6",
"TRAV1-2",
"TRAJ33",
"TRBC2",
"TRAC",
"TGTGCCAGCAGTTACGTCGGGTCTGGGGCCAACGTCCTGACTTTC",
"TGTGCTGTCATGGATAGCAACTATCAGTTAATCTGG",
"CASSYVGSGANVLTF",
"CAVMDSNYQLIW",
"TRBV6-2",
"None",
"TRBJ2-6",
"TRAV1-2",
"TRAJ33",
"TRBC2",
"TRAC",
"True",
"True",
"4.0",
"5.0",
"TRBV6-2",
"TRAV1-2",
"None",
"TRBJ2-6",
"TRAJ33",
"TRBC2",
"TRAC",
"TRBV6-2",
"None",
"TRBJ2-6",
"TRAV1-2",
"TRAJ33",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACCTGGTCAATACC-1",
"abT_VDJ_282_4_3_VJ_1376_2_1",
"4080",
"TRB",
"TRA",
"True",
"True",
"TRBV12-4",
"None",
"TRBJ2-7",
"TRAV22",
"TRAJ4",
"TRBC2",
"TRAC",
"TGTGCCAGCACCCAATCTCTGAGACAGGGTAACGAGCAGTACTTC",
"TGTGCTGTGGAAGGGTTTTCTGGTGGCTACAATAAGCTGATTTTT",
"CASTQSLRQGNEQYF",
"CAVEGFSGGYNKLIF",
"TRBV12-4",
"None",
"TRBJ2-7",
"TRAV22",
"TRAJ4",
"TRBC2",
"TRAC",
"True",
"True",
"9.0",
"19.0",
"TRBV12-4",
"TRAV22",
"None",
"TRBJ2-7",
"TRAJ4",
"TRBC2",
"TRAC",
"TRBV12-4",
"None",
"TRBJ2-7",
"TRAV22",
"TRAJ4",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACCTGGTTCGGCAC-1",
"abT_VDJ_214_4_8_VJ_1113_2_1|abT_VDJ_214_4_8_VJ_1536_2_1",
"4078|4079",
"TRB",
"TRA|TRA",
"True",
"True|True",
"TRBV20-1",
"None",
"TRBJ1-1",
"TRAV8-3|TRAV8-2",
"TRAJ21|TRAJ43",
"TRBC1",
"TRAC|TRAC",
"TGCAGTGCTAGAGGGCGGATGAACACTGAAGCTTTCTTT",
"TGTGCTGTGGAAGTATACAACTTCAACAAATTTTACTTT|TGTGTTGTGAGACCGGAG",
"CSARGRMNTEAFF",
"CAVEVYNFNKFYF|CVVRPE",
"TRBV20-1",
"None",
"TRBJ1-1",
"TRAV8-3|TRAV8-2",
"TRAJ21|TRAJ43",
"TRBC1",
"TRAC|TRAC",
"True",
"True|True",
"15.0",
"18.0",
"TRBV20-1",
"TRAV8-3",
"None",
"TRBJ1-1",
"TRAJ21",
"TRBC1",
"TRAC",
"TRBV20-1",
"None",
"TRBJ1-1",
"TRAV8-3",
"TRAJ21",
"None",
"Multi",
"TRB + Extra VJ",
"Extra pair",
"standard",
"standard"
],
[
"AAACCTGGTTGAACTC-1",
"abT_VDJ_511_2_1_VJ_863_1_1",
"4077",
"TRB",
"TRA",
"True",
"True",
"TRBV4-2",
"None",
"TRBJ2-1",
"TRAV29/DV5",
"TRAJ38",
"TRBC2",
"TRAC",
"TGTGCCAGCAGCCAAGTCATCCAAGGTGAGCAGTTCTTC",
"TGTGCAGCAGGGGTCCGTAATGCTGGCAACAACCGTAAGCTGATTTGG",
"CASSQVIQGEQFF",
"CAAGVRNAGNNRKLIW",
"TRBV4-2",
"None",
"TRBJ2-1",
"TRAV29/DV5",
"TRAJ38",
"TRBC2",
"TRAC",
"True",
"True",
"33.0",
"11.0",
"TRBV4-2",
"TRAV29/DV5",
"None",
"TRBJ2-1",
"TRAJ38",
"TRBC2",
"TRAC",
"TRBV4-2",
"None",
"TRBJ2-1",
"TRAV29/DV5",
"TRAJ38",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACCTGTCACGACTA-1",
"abT_VDJ_25_2_2_VJ_919_1_1",
"4076",
"TRB",
"TRA",
"True",
"True",
"TRBV4-2",
"None",
"TRBJ2-7",
"TRAV12-1",
"TRAJ42",
"TRBC2",
"TRAC",
"TGTGCCAGCAGCCCAGGACGGACCTACGAGCAGTACTTC",
"TGTGTGGTGACCCCTAAGGGGGGAGGAAGCCAAGGAAATCTCATCTTT",
"CASSPGRTYEQYF",
"CVVTPKGGGSQGNLIF",
"TRBV4-2",
"None",
"TRBJ2-7",
"TRAV12-1",
"TRAJ42",
"TRBC2",
"TRAC",
"True",
"True",
"11.0",
"3.0",
"TRBV4-2",
"TRAV12-1",
"None",
"TRBJ2-7",
"TRAJ42",
"TRBC2",
"TRAC",
"TRBV4-2",
"None",
"TRBJ2-7",
"TRAV12-1",
"TRAJ42",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACCTGTCCGAGCCA-1",
"abT_VDJ_445_3_4",
"4075",
"TRB",
"None",
"True",
"None",
"TRBV18",
"None",
"TRBJ2-5",
"None",
"None",
"TRBC2",
"None",
"TGTGCCAGCTCACCGATGGAGCCGATAGGGACCCAGTACTTC",
"None",
"CASSPMEPIGTQYF",
"None",
"TRBV18",
"None",
"TRBJ2-5",
"None",
"None",
"TRBC2",
"None",
"True",
"None",
"13.0",
null,
"TRBV18",
"None",
"None",
"TRBJ2-5",
"None",
"TRBC2",
"None",
"TRBV18",
"None",
"TRBJ2-5",
"None",
"None",
"None",
"None",
"Orphan TRB",
"Orphan VDJ",
"standard",
"None"
],
[
"AAACCTGTCGTCTGAA-1",
"abT_VDJ_148_4_1_VJ_1329_1_1",
"4074",
"TRB",
"TRA",
"True",
"True",
"TRBV6-6",
"None",
"TRBJ1-2",
"TRAV34",
"TRAJ30",
"TRBC1",
"TRAC",
"TGTGCCAGCAGTTACAATCGACCCACAGACTATGGCTACACCTTC",
"TGTGGAGCAGACTTACGTGATGATGACAAGATCATCTTT",
"CASSYNRPTDYGYTF",
"CGADLRDDDKIIF",
"TRBV6-6",
"None",
"TRBJ1-2",
"TRAV34",
"TRAJ30",
"TRBC1",
"TRAC",
"True",
"True",
"21.0",
"12.0",
"TRBV6-6",
"TRAV34",
"None",
"TRBJ1-2",
"TRAJ30",
"TRBC1",
"TRAC",
"TRBV6-6",
"None",
"TRBJ1-2",
"TRAV34",
"TRAJ30",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACCTGTCTTACCGC-1",
"abT_VJ_1092_4_2",
"4073",
"None",
"TRA",
"None",
"True",
"None",
"None",
"None",
"TRAV38-2/DV8",
"TRAJ33",
"None",
"TRAC",
"None",
"TGTGCTCGACAAAAATCGGATAGCAACTATCAGTTAATCTGG",
"None",
"CARQKSDSNYQLIW",
"None",
"None",
"None",
"TRAV38-2/DV8",
"TRAJ33",
"None",
"TRAC",
"None",
"True",
null,
"4.0",
"None",
"TRAV38-2/DV8",
"None",
"None",
"TRAJ33",
"None",
"TRAC",
"None",
"None",
"None",
"TRAV38-2/DV8",
"TRAJ33",
"",
"",
"Orphan TRA",
"Orphan VJ",
"None",
"standard"
],
[
"AAACCTGTCTTGACGA-1",
"abT_VDJ_500_1_2_VJ_856_2_1",
"4071",
"TRB",
"TRA",
"True",
"True",
"TRBV20-1",
"None",
"TRBJ1-6",
"TRAV14/DV4",
"TRAJ28",
"TRBC1",
"TRAC",
"TGCAGTGCTAGCAGGGGAACTTCACCCCTCCACTTT",
"TGTGCAATGAGAGAGGGCGAGGGATACTCTGGGGCTGGGAGTTACCAACTCACTTTC",
"CSASRGTSPLHF",
"CAMREGEGYSGAGSYQLTF",
"TRBV20-1",
"None",
"TRBJ1-6",
"TRAV14/DV4",
"TRAJ28",
"TRBC1",
"TRAC",
"True",
"True",
"16.0",
"7.0",
"TRBV20-1",
"TRAV14/DV4",
"None",
"TRBJ1-6",
"TRAJ28",
"TRBC1",
"TRAC",
"TRBV20-1",
"None",
"TRBJ1-6",
"TRAV14/DV4",
"TRAJ28",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACGGGAGACCCACC-1",
"abT_VDJ_28_4_5_VJ_1198_4_2",
"4061",
"TRB",
"TRA",
"True",
"True",
"TRBV9",
"None",
"TRBJ2-2",
"TRAV38-1",
"TRAJ49",
"TRBC2",
"TRAC",
"TGTGCCAGCAGACTAGACAGGGGGGGGGCCGGGGAGCTGTTTTTT",
"TGTGCTTTCGTGTCCACCGGTAACCAGTTCTATTTT",
"CASRLDRGGAGELFF",
"CAFVSTGNQFYF",
"TRBV9",
"None",
"TRBJ2-2",
"TRAV38-1",
"TRAJ49",
"TRBC2",
"TRAC",
"True",
"True",
"7.0",
"7.0",
"TRBV9",
"TRAV38-1",
"None",
"TRBJ2-2",
"TRAJ49",
"TRBC2",
"TRAC",
"TRBV9",
"None",
"TRBJ2-2",
"TRAV38-1",
"TRAJ49",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACGGGAGGATGTAT-1",
"abT_VDJ_80_6_5_VJ_1337_2_1",
"4070",
"TRB",
"TRA",
"True",
"True",
"TRBV20-1",
"None",
"TRBJ2-1",
"TRAV5",
"TRAJ4",
"TRBC2",
"TRAC",
"TGCAGTGCCAATCCCAGCGGGAGGGAGTGGGGTGAGCAGTTCTTC",
"TGTGCATCAGACTCTGGTGGCTACAATAAGCTGATTTTT",
"CSANPSGREWGEQFF",
"CASDSGGYNKLIF",
"TRBV20-1",
"None",
"TRBJ2-1",
"TRAV5",
"TRAJ4",
"TRBC2",
"TRAC",
"True",
"True",
"17.0",
"15.0",
"TRBV20-1",
"TRAV5",
"None",
"TRBJ2-1",
"TRAJ4",
"TRBC2",
"TRAC",
"TRBV20-1",
"None",
"TRBJ2-1",
"TRAV5",
"TRAJ4",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACGGGAGTGTTTGC-1",
"abT_VDJ_400_7_2_VJ_1411_1_1",
"4069",
"TRB",
"TRA",
"True",
"True",
"TRBV29-1",
"None",
"TRBJ2-1",
"TRAV8-1",
"TRAJ42",
"TRBC2",
"TRAC",
"TGCAGCGTTCGTAGCTACGAGGGAGGTTCCTACAATGAGCAGTTCTTC",
"TGTGCCGCCCGGGGAGGAAGCCAAGGAAATCTCATCTTT",
"CSVRSYEGGSYNEQFF",
"CAARGGSQGNLIF",
"TRBV29-1",
"None",
"TRBJ2-1",
"TRAV8-1",
"TRAJ42",
"TRBC2",
"TRAC",
"True",
"True",
"9.0",
"1.0",
"TRBV29-1",
"TRAV8-1",
"None",
"TRBJ2-1",
"TRAJ42",
"TRBC2",
"TRAC",
"TRBV29-1",
"None",
"TRBJ2-1",
"TRAV8-1",
"TRAJ42",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACGGGGTAAACGCG-1",
"abT_VDJ_188_2_3_VJ_381_1_1",
"4068",
"TRB",
"TRA",
"True",
"True",
"TRBV12-4",
"None",
"TRBJ1-2",
"TRAV19",
"TRAJ17",
"TRBC1",
"TRAC",
"TGTGCCAGCAGTCTCCGACAGGATTGGGGCTACACCTTC",
"TGTGCTCTGATCAAAGCTGCAGGCAACAAGCTAACTTTT",
"CASSLRQDWGYTF",
"CALIKAAGNKLTF",
"TRBV12-4",
"None",
"TRBJ1-2",
"TRAV19",
"TRAJ17",
"TRBC1",
"TRAC",
"True",
"True",
"8.0",
"3.0",
"TRBV12-4",
"TRAV19",
"None",
"TRBJ1-2",
"TRAJ17",
"TRBC1",
"TRAC",
"TRBV12-4",
"None",
"TRBJ1-2",
"TRAV19",
"TRAJ17",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACGGGGTAGCCTCG-1",
"abT_VJ_1180_4_5",
"4067",
"None",
"TRA",
"None",
"True",
"None",
"None",
"None",
"TRAV1-2",
"TRAJ20",
"None",
"TRAC",
"None",
"TGTGCTGTGAAGCGGGGCGACTACAAGCTCAGCTTT",
"None",
"CAVKRGDYKLSF",
"None",
"None",
"None",
"TRAV1-2",
"TRAJ20",
"None",
"TRAC",
"None",
"True",
null,
"8.0",
"None",
"TRAV1-2",
"None",
"None",
"TRAJ20",
"None",
"TRAC",
"None",
"None",
"None",
"TRAV1-2",
"TRAJ20",
"",
"",
"Orphan TRA",
"Orphan VJ",
"None",
"standard"
],
[
"AAACGGGTCACGATGT-1",
"abT_VDJ_509_8_1_VJ_1086_2_2",
"4066",
"TRB",
"TRA",
"True",
"True",
"TRBV6-5",
"None",
"TRBJ2-1",
"TRAV27",
"TRAJ40",
"TRBC2",
"TRAC",
"TGTGCCAGCAGTTACTCCGTACTAGCGGGGGGGCATCAGTGGGGGGGGTGTGAGCAGTTCTTC",
"TGTGCAGGAGACTACTCAGGAACCTACAAATACATCTTT",
"CASSYSVLAGGHQWGGCEQFF",
"CAGDYSGTYKYIF",
"TRBV6-5",
"None",
"TRBJ2-1",
"TRAV27",
"TRAJ40",
"TRBC2",
"TRAC",
"True",
"True",
"5.0",
"4.0",
"TRBV6-5",
"TRAV27",
"None",
"TRBJ2-1",
"TRAJ40",
"TRBC2",
"TRAC",
"TRBV6-5",
"None",
"TRBJ2-1",
"TRAV27",
"TRAJ40",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACGGGTCAGGTAAA-1",
"abT_VDJ_393_8_1_VJ_553_1_1",
"4065",
"TRB",
"TRA",
"True",
"True",
"TRBV6-2",
"None",
"TRBJ2-7",
"TRAV2",
"TRAJ5",
"TRBC2",
"TRAC",
"TGTGCCAGCAGTTCTCCGGGACAGGGGACTAAAGTCCCCTACGAGCAGTACTTC",
"TGCCCCGACACGGGCAGGAGAGCACTTACTTTT",
"CASSSPGQGTKVPYEQYF",
"CPDTGRRALTF",
"TRBV6-2",
"None",
"TRBJ2-7",
"TRAV2",
"TRAJ5",
"TRBC2",
"TRAC",
"True",
"True",
"10.0",
"10.0",
"TRBV6-2",
"TRAV2",
"None",
"TRBJ2-7",
"TRAJ5",
"TRBC2",
"TRAC",
"TRBV6-2",
"None",
"TRBJ2-7",
"TRAV2",
"TRAJ5",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACGGGTCCGCGCAA-1",
"abT_VDJ_327_4_4_VJ_1263_1_1",
"4064",
"TRB",
"TRA",
"True",
"True",
"TRBV7-9",
"None",
"TRBJ2-1",
"TRAV10",
"TRAJ40",
"TRBC2",
"TRAC",
"TGTGCCAGCAGCTCAGGAAATTCCTACAATGAGCAGTTCTTC",
"TGTGTGGTGAGCGCGGGAACCTACAAATACATCTTT",
"CASSSGNSYNEQFF",
"CVVSAGTYKYIF",
"TRBV7-9",
"None",
"TRBJ2-1",
"TRAV10",
"TRAJ40",
"TRBC2",
"TRAC",
"True",
"True",
"26.0",
"7.0",
"TRBV7-9",
"TRAV10",
"None",
"TRBJ2-1",
"TRAJ40",
"TRBC2",
"TRAC",
"TRBV7-9",
"None",
"TRBJ2-1",
"TRAV10",
"TRAJ40",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACGGGTCGGATGTT-1",
"abT_VDJ_429_1_1_VJ_1115_2_1",
"4063",
"TRB",
"TRA",
"True",
"True",
"TRBV28",
"None",
"TRBJ1-4",
"TRAV38-1",
"TRAJ41",
"TRBC1",
"TRAC",
"TGTGCCAGCAGTTTTCTTGAAAAACTGTTTTTT",
"TGTGCTTTCAGTTTGAACTCAAATTCCGGGTATGCACTCAACTTC",
"CASSFLEKLFF",
"CAFSLNSNSGYALNF",
"TRBV28",
"None",
"TRBJ1-4",
"TRAV38-1",
"TRAJ41",
"TRBC1",
"TRAC",
"True",
"True",
"9.0",
"3.0",
"TRBV28",
"TRAV38-1",
"None",
"TRBJ1-4",
"TRAJ41",
"TRBC1",
"TRAC",
"TRBV28",
"None",
"TRBJ1-4",
"TRAV38-1",
"TRAJ41",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAACGGGTCTAACGGT-1",
"abT_VDJ_62_2_1_VJ_1573_1_1",
"4062",
"TRB",
"TRA",
"True",
"True",
"TRBV20-1",
"None",
"TRBJ2-5",
"TRAV29/DV5",
"TRAJ58",
"TRBC2",
"TRAC",
"TGCAGTGCTTCTTACCATACGGCCCAGTACTTC",
"TGTGCAGCAAGCTGGAAAGGTAGAGGGGAAACCAGTGGCTCTAGGTTGACCTTT",
"CSASYHTAQYF",
"CAASWKGRGETSGSRLTF",
"TRBV20-1",
"None",
"TRBJ2-5",
"TRAV29/DV5",
"TRAJ58",
"TRBC2",
"TRAC",
"True",
"True",
"26.0",
"7.0",
"TRBV20-1",
"TRAV29/DV5",
"None",
"TRBJ2-5",
"TRAJ58",
"TRBC2",
"TRAC",
"TRBV20-1",
"None",
"TRBJ2-5",
"TRAV29/DV5",
"TRAJ58",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGATGAGCAGACTG-1",
"abT_VDJ_359_1_7_VJ_1105_1_1",
"4082",
"TRB",
"TRA",
"True",
"True",
"TRBV2",
"None",
"TRBJ1-5",
"TRAV24",
"TRAJ49",
"TRBC1",
"TRAC",
"TGTGCCAGCACTAAGGACAGGGAGAAGCCCCAGCATTTT",
"TGTGCCTTTAGTACCGGTAACCAGTTCTATTTT",
"CASTKDREKPQHF",
"CAFSTGNQFYF",
"TRBV2",
"None",
"TRBJ1-5",
"TRAV24",
"TRAJ49",
"TRBC1",
"TRAC",
"True",
"True",
"11.0",
"11.0",
"TRBV2",
"TRAV24",
"None",
"TRBJ1-5",
"TRAJ49",
"TRBC1",
"TRAC",
"TRBV2",
"None",
"TRBJ1-5",
"TRAV24",
"TRAJ49",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGATGAGGTGCAAC-1",
"abT_VDJ_212_4_3_VJ_717_5_1",
"4083",
"TRB",
"TRA",
"True",
"True",
"TRBV5-1",
"None",
"TRBJ2-2",
"TRAV41",
"TRAJ33",
"TRBC2",
"TRAC",
"TGCGCCAGCAGCTGGGGGGGACAGGGGAGCACCGGGGAGCTGTTTTTT",
"TGTGCTGTCAGATCCAGGTTCCACATGGATAGCAACTATCAGTTAATCTGG",
"CASSWGGQGSTGELFF",
"CAVRSRFHMDSNYQLIW",
"TRBV5-1",
"None",
"TRBJ2-2",
"TRAV41",
"TRAJ33",
"TRBC2",
"TRAC",
"True",
"True",
"7.0",
"7.0",
"TRBV5-1",
"TRAV41",
"None",
"TRBJ2-2",
"TRAJ33",
"TRBC2",
"TRAC",
"TRBV5-1",
"None",
"TRBJ2-2",
"TRAV41",
"TRAJ33",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGATGAGTGGGATC-1",
"abT_VDJ_194_6_1_VJ_1279_4_3",
"4084",
"TRB",
"TRA",
"True",
"True",
"TRBV11-2",
"None",
"TRBJ1-2",
"TRAV29/DV5",
"TRAJ53",
"TRBC1",
"TRAC",
"TGTGCCAGCAGCTCCGTAAGACAGGGCAAACGTGAGGTATATGGCTACACCTTC",
"TGTGCAGCAAGCAATAGTGGAGGTAGCAACTATAAACTGACATTT",
"CASSSVRQGKREVYGYTF",
"CAASNSGGSNYKLTF",
"TRBV11-2",
"None",
"TRBJ1-2",
"TRAV29/DV5",
"TRAJ53",
"TRBC1",
"TRAC",
"True",
"True",
"7.0",
"6.0",
"TRBV11-2",
"TRAV29/DV5",
"None",
"TRBJ1-2",
"TRAJ53",
"TRBC1",
"TRAC",
"TRBV11-2",
"None",
"TRBJ1-2",
"TRAV29/DV5",
"TRAJ53",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGATGCATCTCGCT-1",
"abT_VDJ_412_6_3_VJ_361_2_1",
"4085",
"TRB",
"TRA",
"True",
"True",
"TRBV5-1",
"None",
"TRBJ2-3",
"TRAV17",
"TRAJ21",
"TRBC2",
"TRAC",
"TGCGCCAGCAGCTTGAACCTCTTGGGGGGTTCCACAGATACGCAGTATTTT",
"TGTGCTACGGACGTACCCCCCAACTTCAACAAATTTTACTTT",
"CASSLNLLGGSTDTQYF",
"CATDVPPNFNKFYF",
"TRBV5-1",
"None",
"TRBJ2-3",
"TRAV17",
"TRAJ21",
"TRBC2",
"TRAC",
"True",
"True",
"3.0",
"2.0",
"TRBV5-1",
"TRAV17",
"None",
"TRBJ2-3",
"TRAJ21",
"TRBC2",
"TRAC",
"TRBV5-1",
"None",
"TRBJ2-3",
"TRAV17",
"TRAJ21",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGATGGTACTTCTT-1",
"abT_VDJ_421_3_1_VJ_203_3_1",
"4104",
"TRB",
"TRA",
"True",
"True",
"TRBV24-1",
"None",
"TRBJ2-6",
"TRAV19",
"TRAJ13",
"TRBC2",
"TRAC",
"TGTGCCACCAGTGATTCACTATCTGGGGCCAACGTCCTGACTTTC",
"TGTGCTCTGCTGGCTTCTGGGGGTTACCAGAAAGTTACCTTT",
"CATSDSLSGANVLTF",
"CALLASGGYQKVTF",
"TRBV24-1",
"None",
"TRBJ2-6",
"TRAV19",
"TRAJ13",
"TRBC2",
"TRAC",
"True",
"True",
"22.0",
"4.0",
"TRBV24-1",
"TRAV19",
"None",
"TRBJ2-6",
"TRAJ13",
"TRBC2",
"TRAC",
"TRBV24-1",
"None",
"TRBJ2-6",
"TRAV19",
"TRAJ13",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGATGGTCCCTTGT-1",
"abT_VDJ_43_5_1_VJ_248_3_3",
"4103",
"TRB",
"TRA",
"True",
"True",
"TRBV7-2",
"None",
"TRBJ2-3",
"TRAV3",
"TRAJ30",
"TRBC2",
"TRAC",
"TGTGCCAGCAATACTAGGGGTAGGAGCACAGATACGCAGTATTTT",
"TGTGCTGTGCCCCCGAGGAACAGAGATGACAAGATCATCTTT",
"CASNTRGRSTDTQYF",
"CAVPPRNRDDKIIF",
"TRBV7-2",
"None",
"TRBJ2-3",
"TRAV3",
"TRAJ30",
"TRBC2",
"TRAC",
"True",
"True",
"18.0",
"8.0",
"TRBV7-2",
"TRAV3",
"None",
"TRBJ2-3",
"TRAJ30",
"TRBC2",
"TRAC",
"TRBV7-2",
"None",
"TRBJ2-3",
"TRAV3",
"TRAJ30",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGATGTCGGAATCT-1",
"abT_VDJ_292_2_1_VJ_1385_2_1|abT_VDJ_292_2_1_VJ_550_1_1",
"4101|4102",
"TRB",
"TRA|TRA",
"True",
"True|True",
"TRBV14",
"None",
"TRBJ2-3",
"TRAV16|TRAV3",
"TRAJ5|TRAJ26",
"TRBC2",
"TRAC|TRAC",
"TGTGCCAGCAGCCCGGGGGGCCAGAATACGCAGTATTTT",
"TGTGCTTCATACACGGGCAGGAGAGCACTTACTTTT|TGTGCTGTGACCCACTATGGTCAGAATTTTGTCTTT",
"CASSPGGQNTQYF",
"CASYTGRRALTF|CAVTHYGQNFVF",
"TRBV14",
"None",
"TRBJ2-3",
"TRAV16|TRAV3",
"TRAJ5|TRAJ26",
"TRBC2",
"TRAC|TRAC",
"True",
"True|True",
"11.0",
"10.0",
"TRBV14",
"TRAV16",
"None",
"TRBJ2-3",
"TRAJ5",
"TRBC2",
"TRAC",
"TRBV14",
"None",
"TRBJ2-3",
"TRAV16",
"TRAJ5",
"None",
"Multi",
"TRB + Extra VJ",
"Extra pair",
"standard",
"standard"
],
[
"AAAGATGTCTGTCTCG-1",
"abT_VDJ_260_3_2_VJ_818_1_1",
"4100",
"TRB",
"TRA",
"True",
"True",
"TRBV12-4",
"None",
"TRBJ2-1",
"TRAV27",
"TRAJ6",
"TRBC2",
"TRAC",
"TGTGCCAGCAGTTTCGGGGGTCTCTACAATGAGCAGTTCTTC",
"TGTGCAGGAGGGAGAGGAAGCTACATACCTACATTT",
"CASSFGGLYNEQFF",
"CAGGRGSYIPTF",
"TRBV12-4",
"None",
"TRBJ2-1",
"TRAV27",
"TRAJ6",
"TRBC2",
"TRAC",
"True",
"True",
"2.0",
"5.0",
"TRBV12-4",
"TRAV27",
"None",
"TRBJ2-1",
"TRAJ6",
"TRBC2",
"TRAC",
"TRBV12-4",
"None",
"TRBJ2-1",
"TRAV27",
"TRAJ6",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGCAAAGAGGGATA-1",
"abT_VDJ_57_3_1_VJ_867_2_1",
"4099",
"TRB",
"TRA",
"True",
"True",
"TRBV7-9",
"None",
"TRBJ1-5",
"TRAV4",
"TRAJ29",
"TRBC1",
"TRAC",
"TGTGCCAGCAGCTTGGGGACAGGAGGACAGCCCCAGCATTTT",
"TGCCTCGTGGGTGCCTGGAATTCAGGAAACACACCTCTTGTCTTT",
"CASSLGTGGQPQHF",
"CLVGAWNSGNTPLVF",
"TRBV7-9",
"None",
"TRBJ1-5",
"TRAV4",
"TRAJ29",
"TRBC1",
"TRAC",
"True",
"True",
"17.0",
"9.0",
"TRBV7-9",
"TRAV4",
"None",
"TRBJ1-5",
"TRAJ29",
"TRBC1",
"TRAC",
"TRBV7-9",
"None",
"TRBJ1-5",
"TRAV4",
"TRAJ29",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGCAAAGTAGGCCA-1",
"abT_VDJ_255_3_2_VJ_1182_1_3",
"4098",
"TRB",
"TRA",
"True",
"True",
"TRBV2",
"None",
"TRBJ1-1",
"TRAV8-6",
"TRAJ5",
"TRBC1",
"TRAC",
"TGTGCCAGCAGGGACAGGGACTCTGAAGCTTTCTTT",
"TGTGCTGTGAGTGAGAGGGGCAGGAGAGCACTTACTTTT",
"CASRDRDSEAFF",
"CAVSERGRRALTF",
"TRBV2",
"None",
"TRBJ1-1",
"TRAV8-6",
"TRAJ5",
"TRBC1",
"TRAC",
"True",
"True",
"7.0",
"4.0",
"TRBV2",
"TRAV8-6",
"None",
"TRBJ1-1",
"TRAJ5",
"TRBC1",
"TRAC",
"TRBV2",
"None",
"TRBJ1-1",
"TRAV8-6",
"TRAJ5",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGCAAAGTGCAAGC-1",
"abT_VDJ_139_4_4_VJ_1481_2_1",
"4097",
"TRB",
"TRA",
"True",
"True",
"TRBV24-1",
"None",
"TRBJ2-2",
"TRAV10",
"TRAJ6",
"TRBC2",
"TRAC",
"TGTGCCACCAGTTCCCTAGCGGTTCACACCGGGGAGCTGTTTTTT",
"TGTGTGGTAGGGACAGGAGGAAGCTACATACCTACATTT",
"CATSSLAVHTGELFF",
"CVVGTGGSYIPTF",
"TRBV24-1",
"None",
"TRBJ2-2",
"TRAV10",
"TRAJ6",
"TRBC2",
"TRAC",
"True",
"True",
"10.0",
"3.0",
"TRBV24-1",
"TRAV10",
"None",
"TRBJ2-2",
"TRAJ6",
"TRBC2",
"TRAC",
"TRBV24-1",
"None",
"TRBJ2-2",
"TRAV10",
"TRAJ6",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGCAAGTAAACACA-1",
"abT_VDJ_496_4_1_VJ_706_3_1",
"4096",
"TRB",
"TRA",
"True",
"True",
"TRBV11-2",
"None",
"TRBJ1-3",
"TRAV22",
"TRAJ28",
"TRBC1",
"TRAC",
"TGTGCCAGCAGCCCCCAGGGGTACTCTGGAAACACCATATATTTT",
"TGTGCCCTTTGGAGGGGGGCTGGGAGTTACCAACTCACTTTC",
"CASSPQGYSGNTIYF",
"CALWRGAGSYQLTF",
"TRBV11-2",
"None",
"TRBJ1-3",
"TRAV22",
"TRAJ28",
"TRBC1",
"TRAC",
"True",
"True",
"4.0",
"2.0",
"TRBV11-2",
"TRAV22",
"None",
"TRBJ1-3",
"TRAJ28",
"TRBC1",
"TRAC",
"TRBV11-2",
"None",
"TRBJ1-3",
"TRAV22",
"TRAJ28",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGCAAGTTCAACCA-1",
"abT_VDJ_345_4_6_VJ_1350_1_1",
"4095",
"TRB",
"TRA",
"True",
"True",
"TRBV6-6",
"None",
"TRBJ1-1",
"TRAV17",
"TRAJ29",
"TRBC1",
"TRAC",
"TGTGCCAGCAGAACCCCAGGGGAAACTGAAGCTTTCTTT",
"TGTGCTACGGGTAAAGGAAACACACCTCTTGTCTTT",
"CASRTPGETEAFF",
"CATGKGNTPLVF",
"TRBV6-6",
"None",
"TRBJ1-1",
"TRAV17",
"TRAJ29",
"TRBC1",
"TRAC",
"True",
"True",
"17.0",
"7.0",
"TRBV6-6",
"TRAV17",
"None",
"TRBJ1-1",
"TRAJ29",
"TRBC1",
"TRAC",
"TRBV6-6",
"None",
"TRBJ1-1",
"TRAV17",
"TRAJ29",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGCAAGTTCAGGCC-1",
"abT_VDJ_296_1_1_VJ_525_1_1",
"4094",
"TRB",
"TRA",
"True",
"True",
"TRBV7-3",
"None",
"TRBJ1-5",
"TRAV12-3",
"TRAJ35",
"TRBC1",
"TRAC",
"TGTGCCAGCAGCTTAACCTATGATCAGCCCCAGCATTTT",
"TGTGCAATGAGAGAGGTAGGCTTTGGGAATGTGCTGCATTGC",
"CASSLTYDQPQHF",
"CAMREVGFGNVLHC",
"TRBV7-3",
"None",
"TRBJ1-5",
"TRAV12-3",
"TRAJ35",
"TRBC1",
"TRAC",
"True",
"True",
"15.0",
"4.0",
"TRBV7-3",
"TRAV12-3",
"None",
"TRBJ1-5",
"TRAJ35",
"TRBC1",
"TRAC",
"TRBV7-3",
"None",
"TRBJ1-5",
"TRAV12-3",
"TRAJ35",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGCAAGTTTACTCT-1",
"abT_VDJ_163_3_1_VJ_125_3_1|abT_VDJ_311_4_6_VJ_125_3_1",
"4092|4093",
"TRB|TRB",
"TRA",
"True|True",
"True",
"TRBV4-1|TRBV6-5",
"None",
"TRBJ1-5|TRBJ1-4",
"TRAV21",
"TRAJ35",
"TRBC1|TRBC1",
"TRAC",
"TGCGCCAGCAGCCAAGACCCGGGGTTCGGCCAGCCCCAGCATTTT|TGTGCCAGCAGTTCTCCGAGGGACGGAGGTGAAAAACTGTTTTTT",
"TGTGCTGTCCTGGACTCGATAGGCTTTGGGAATGTGCTGCATTGC",
"CASSQDPGFGQPQHF|CASSSPRDGGEKLFF",
"CAVLDSIGFGNVLHC",
"TRBV4-1|TRBV6-5",
"None",
"TRBJ1-5|TRBJ1-4",
"TRAV21",
"TRAJ35",
"TRBC1|TRBC1",
"TRAC",
"True|True",
"True",
"17.0",
"11.0",
"TRBV4-1",
"TRAV21",
"None",
"TRBJ1-5",
"TRAJ35",
"TRBC1",
"TRAC",
"TRBV4-1",
"None",
"TRBJ1-5",
"TRAV21",
"TRAJ35",
"None|None",
"Multi",
"Extra VDJ + TRA",
"Extra pair",
"standard",
"standard"
],
[
"AAAGCAATCAGTTCGA-1",
"abT_VDJ_119_5_6_VJ_319_3_1|abT_VDJ_119_5_6_VJ_43_3_1",
"68|69",
"TRB",
"TRA|TRA",
"True",
"True|True",
"TRBV6-5",
"None",
"TRBJ2-3",
"TRAV8-4|TRAV13-1",
"TRAJ22|TRAJ45",
"TRBC2",
"TRAC|TRAC",
"TGTGCCAGCAGGGGGGGACTAGCGGGCACAGATACGCAGTATTTT",
"TGTGCTGTGACCATTTCTGGTTCTGCAAGGCAACTGACCTTT|TGTGCAGCAAATTCAGGAGGAGGTGCTGACGGACTCACCTTT",
"CASRGGLAGTDTQYF",
"CAVTISGSARQLTF|CAANSGGGADGLTF",
"TRBV6-5",
"None",
"TRBJ2-3",
"TRAV8-4|TRAV13-1",
"TRAJ22|TRAJ45",
"TRBC2",
"TRAC|TRAC",
"True",
"True|True",
"6.0",
"14.0",
"TRBV6-5",
"TRAV8-4",
"None",
"TRBJ2-3",
"TRAJ22",
"TRBC2",
"TRAC",
"TRBV6-5",
"None",
"TRBJ2-3",
"TRAV8-4",
"TRAJ22",
"None",
"Multi",
"TRB + Extra VJ",
"Extra pair",
"standard",
"standard"
],
[
"AAAGCAATCATATCGG-1",
"abT_VDJ_22_1_2_VJ_1505_4_1",
"4091",
"TRB",
"TRA",
"True",
"True",
"TRBV6-5",
"None",
"TRBJ2-7",
"TRAV25",
"TRAJ53",
"TRBC2",
"TRAC",
"TGTGCCAGCAGTCCCCCGGGGGTCGAGCAGTACTTC",
"TGTGCAGGGCCGGGGAGTGGAGGTAGCAACTATAAACTGACATTT",
"CASSPPGVEQYF",
"CAGPGSGGSNYKLTF",
"TRBV6-5",
"None",
"TRBJ2-7",
"TRAV25",
"TRAJ53",
"TRBC2",
"TRAC",
"True",
"True",
"15.0",
"3.0",
"TRBV6-5",
"TRAV25",
"None",
"TRBJ2-7",
"TRAJ53",
"TRBC2",
"TRAC",
"TRBV6-5",
"None",
"TRBJ2-7",
"TRAV25",
"TRAJ53",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGCAATCTGAGTGT-1",
"abT_VDJ_409_8_1_VJ_373_4_2",
"4090",
"TRB",
"TRA",
"True",
"True",
"TRBV6-6",
"None",
"TRBJ2-7",
"TRAV35",
"TRAJ49",
"TRBC2",
"TRAC",
"TGTGCCAGCAGTTCCCAGGGGACTAGCGGGAGACTAGAACGCTACGAGCAGTACTTC",
"TGTGCTGGCTACGACCCACGTGGAAACCAGTTCTATTTT",
"CASSSQGTSGRLERYEQYF",
"CAGYDPRGNQFYF",
"TRBV6-6",
"None",
"TRBJ2-7",
"TRAV35",
"TRAJ49",
"TRBC2",
"TRAC",
"True",
"True",
"9.0",
"11.0",
"TRBV6-6",
"TRAV35",
"None",
"TRBJ2-7",
"TRAJ49",
"TRBC2",
"TRAC",
"TRBV6-6",
"None",
"TRBJ2-7",
"TRAV35",
"TRAJ49",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGTAGAGCCAGTAG-1",
"abT_VDJ_45_1_1_VJ_1123_1_2|abT_VDJ_45_1_1_VJ_451_1_1",
"8|9",
"TRB",
"TRA|TRA",
"True",
"True|True",
"TRBV4-1",
"None",
"TRBJ1-1",
"TRAV13-1|TRAV20",
"TRAJ42|TRAJ45",
"TRBC1",
"TRAC|TRAC",
"TGCGCCAGCAGCCTGACAGGCTCTGAAGCTTTCTTT",
"TGTGCAGCAAGTTCTTCCCATGGAGGAAGCCAAGGAAATCTCATCTTT|TGTGCTGTGCAGGGGTATTCAGGAGGAGGTGCTGACGGACTCACCTTT",
"CASSLTGSEAFF",
"CAASSSHGGSQGNLIF|CAVQGYSGGGADGLTF",
"TRBV4-1",
"None",
"TRBJ1-1",
"TRAV13-1|TRAV20",
"TRAJ42|TRAJ45",
"TRBC1",
"TRAC|TRAC",
"True",
"True|True",
"7.0",
"12.0",
"TRBV4-1",
"TRAV13-1",
"None",
"TRBJ1-1",
"TRAJ42",
"TRBC1",
"TRAC",
"TRBV4-1",
"None",
"TRBJ1-1",
"TRAV13-1",
"TRAJ42",
"None",
"Multi",
"TRB + Extra VJ",
"Extra pair",
"standard",
"standard"
],
[
"AAAGTAGCAAGGCTCC-1",
"abT_VDJ_87_2_2_VJ_1049_1_1|abT_VDJ_87_2_2_VJ_640_2_2",
"4088|4089",
"TRB",
"TRA|TRA",
"True",
"True|True",
"TRBV12-5",
"None",
"TRBJ2-2",
"TRAV27|TRAV12-1",
"TRAJ4|TRAJ31",
"TRBC2",
"TRAC|TRAC",
"TGTGCTAGTTTTTCCGACTCGAACACCGGGGAGCTGTTTTTT",
"TGTGCAGGTACCCTTACTCTTTCTGGTGGCTACAATAAGCTGATTTTT|TGTGTGGTGAACGATGCCAGACTCATGTTT",
"CASFSDSNTGELFF",
"CAGTLTLSGGYNKLIF|CVVNDARLMF",
"TRBV12-5",
"None",
"TRBJ2-2",
"TRAV27|TRAV12-1",
"TRAJ4|TRAJ31",
"TRBC2",
"TRAC|TRAC",
"True",
"True|True",
"19.0",
"17.0",
"TRBV12-5",
"TRAV27",
"None",
"TRBJ2-2",
"TRAJ4",
"TRBC2",
"TRAC",
"TRBV12-5",
"None",
"TRBJ2-2",
"TRAV27",
"TRAJ4",
"None",
"Multi",
"TRB + Extra VJ",
"Extra pair",
"standard",
"standard"
],
[
"AAAGTAGCAATGGTCT-1",
"abT_VDJ_405_3_2_VJ_341_4_1",
"4087",
"TRB",
"TRA",
"True",
"True",
"TRBV18",
"None",
"TRBJ1-2",
"TRAV12-2",
"TRAJ3",
"TRBC1",
"TRAC",
"TGTGCCAGCTCACCTATCACTACTGGGGACTATGGCTACACCTTC",
"TGTGCCGTGAACAGGCTTAGCAGTGCTTCCAAGATAATCTTT",
"CASSPITTGDYGYTF",
"CAVNRLSSASKIIF",
"TRBV18",
"None",
"TRBJ1-2",
"TRAV12-2",
"TRAJ3",
"TRBC1",
"TRAC",
"True",
"True",
"5.0",
"5.0",
"TRBV18",
"TRAV12-2",
"None",
"TRBJ1-2",
"TRAJ3",
"TRBC1",
"TRAC",
"TRBV18",
"None",
"TRBJ1-2",
"TRAV12-2",
"TRAJ3",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGTAGCAGCTGCAC-1",
"abT_VDJ_307_3_3_VJ_136_1_2",
"4086",
"TRB",
"TRA",
"True",
"True",
"TRBV5-1",
"None",
"TRBJ2-7",
"TRAV13-2",
"TRAJ16",
"TRBC2",
"TRAC",
"TGCGCCAGCAGCCCAGGGGGCTCCTACGAGCAGTACTTC",
"TGTGCAGAGAAACTTAATGGCCAGAAGCTGCTCTTT",
"CASSPGGSYEQYF",
"CAEKLNGQKLLF",
"TRBV5-1",
"None",
"TRBJ2-7",
"TRAV13-2",
"TRAJ16",
"TRBC2",
"TRAC",
"True",
"True",
"11.0",
"6.0",
"TRBV5-1",
"TRAV13-2",
"None",
"TRBJ2-7",
"TRAJ16",
"TRBC2",
"TRAC",
"TRBV5-1",
"None",
"TRBJ2-7",
"TRAV13-2",
"TRAJ16",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGTAGGTACCAGTT-1",
"abT_VDJ_214_4_7_VJ_1533_1_1",
"4072",
"TRB",
"TRA",
"True",
"True",
"TRBV20-1",
"None",
"TRBJ1-1",
"TRAV12-2",
"TRAJ21",
"TRBC1",
"TRAC",
"TGCAGTGCTCCAACAGGGGCGGGGACTGAAGCTTTCTTT",
"TGTGCCGTGAGGGACTTCAACAAATTTTACTTT",
"CSAPTGAGTEAFF",
"CAVRDFNKFYF",
"TRBV20-1",
"None",
"TRBJ1-1",
"TRAV12-2",
"TRAJ21",
"TRBC1",
"TRAC",
"True",
"True",
"10.0",
"2.0",
"TRBV20-1",
"TRAV12-2",
"None",
"TRBJ1-1",
"TRAJ21",
"TRBC1",
"TRAC",
"TRBV20-1",
"None",
"TRBJ1-1",
"TRAV12-2",
"TRAJ21",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGTAGGTCATACTG-1",
"abT_VDJ_134_1_2_VJ_491_2_1",
"4059",
"TRB",
"TRA",
"True",
"True",
"TRBV4-3",
"None",
"TRBJ2-3",
"TRAV38-1",
"TRAJ28",
"TRBC2",
"TRAC",
"TGCGCCAGCAGCCAAGATCCATTCGATACGCAGTATTTT",
"TGTGCTTTCATGAAGCATGTGTCCGGGGCTGGGAGTTACCAACTCACTTTC",
"CASSQDPFDTQYF",
"CAFMKHVSGAGSYQLTF",
"TRBV4-3",
"None",
"TRBJ2-3",
"TRAV38-1",
"TRAJ28",
"TRBC2",
"TRAC",
"True",
"True",
"15.0",
"3.0",
"TRBV4-3",
"TRAV38-1",
"None",
"TRBJ2-3",
"TRAJ28",
"TRBC2",
"TRAC",
"TRBV4-3",
"None",
"TRBJ2-3",
"TRAV38-1",
"TRAJ28",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGTAGGTCCGAACC-1",
"abT_VDJ_142_1_1_VJ_1367_2_1",
"4025",
"TRB",
"TRA",
"True",
"True",
"TRBV18",
"None",
"TRBJ2-7",
"TRAV12-3",
"TRAJ39",
"TRBC2",
"TRAC",
"TGTGCCAGCTCCCCCCAGAGCTACGAGCAGTACTTC",
"TGTGCAATGAGCCTCAATAATGCAGGCAACATGCTCACCTTT",
"CASSPQSYEQYF",
"CAMSLNNAGNMLTF",
"TRBV18",
"None",
"TRBJ2-7",
"TRAV12-3",
"TRAJ39",
"TRBC2",
"TRAC",
"True",
"True",
"7.0",
"2.0",
"TRBV18",
"TRAV12-3",
"None",
"TRBJ2-7",
"TRAJ39",
"TRBC2",
"TRAC",
"TRBV18",
"None",
"TRBJ2-7",
"TRAV12-3",
"TRAJ39",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGTAGGTCTGCCAG-1",
"abT_VDJ_501_2_1_VJ_688_1_1",
"4058",
"TRB",
"TRA",
"True",
"True",
"TRBV12-3",
"None",
"TRBJ2-6",
"TRAV2",
"TRAJ22",
"TRBC2",
"TRAC",
"TGTGCCAGCAGTTCCAGACAGGTCTTCTCTGGGGCCAACGTCCTGACTTTC",
"TGTGCTGTTACTTCTGGTTCTGCAAGGCAACTGACCTTT",
"CASSSRQVFSGANVLTF",
"CAVTSGSARQLTF",
"TRBV12-3",
"None",
"TRBJ2-6",
"TRAV2",
"TRAJ22",
"TRBC2",
"TRAC",
"True",
"True",
"12.0",
"3.0",
"TRBV12-3",
"TRAV2",
"None",
"TRBJ2-6",
"TRAJ22",
"TRBC2",
"TRAC",
"TRBV12-3",
"None",
"TRBJ2-6",
"TRAV2",
"TRAJ22",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGTAGGTTCAGGCC-1",
"abT_VDJ_63_2_3_VJ_444_1_1",
"4034",
"TRB",
"TRA",
"True",
"True",
"TRBV9",
"None",
"TRBJ1-1",
"TRAV3",
"TRAJ47",
"TRBC1",
"TRAC",
"TGTGCCAGCAGCTCGGGACAGCACACTGAAGCTTTCTTT",
"TGTGCTGTGAGAGCCCGGGAATATGGAAACAAACTGGTCTTT",
"CASSSGQHTEAFF",
"CAVRAREYGNKLVF",
"TRBV9",
"None",
"TRBJ1-1",
"TRAV3",
"TRAJ47",
"TRBC1",
"TRAC",
"True",
"True",
"10.0",
"9.0",
"TRBV9",
"TRAV3",
"None",
"TRBJ1-1",
"TRAJ47",
"TRBC1",
"TRAC",
"TRBV9",
"None",
"TRBJ1-1",
"TRAV3",
"TRAJ47",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGTAGTCAGGCAAG-1",
"abT_VDJ_454_2_1_VJ_271_1_1",
"4033",
"TRB",
"TRA",
"True",
"True",
"TRBV3-1",
"None",
"TRBJ2-7",
"TRAV8-4",
"TRAJ56",
"TRBC2",
"TRAC",
"TGTGCCAGCAGCCTTAGCTCCTACGAGCAGTACTTC",
"TGTGCTGTATATACTGGAGCCAATAGTAAGCTGACATTT",
"CASSLSSYEQYF",
"CAVYTGANSKLTF",
"TRBV3-1",
"None",
"TRBJ2-7",
"TRAV8-4",
"TRAJ56",
"TRBC2",
"TRAC",
"True",
"True",
"20.0",
"5.0",
"TRBV3-1",
"TRAV8-4",
"None",
"TRBJ2-7",
"TRAJ56",
"TRBC2",
"TRAC",
"TRBV3-1",
"None",
"TRBJ2-7",
"TRAV8-4",
"TRAJ56",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
],
[
"AAAGTAGTCGCATGGC-1",
"abT_VDJ_242_3_3_VJ_1311_1_2",
"4032",
"TRB",
"TRA",
"True",
"True",
"TRBV7-2",
"None",
"TRBJ1-4",
"TRAV29/DV5",
"TRAJ36",
"TRBC1",
"TRAC",
"TGTGCCAGCAGCTTAGCCAGGGCGTCTAATGAAAAACTGTTTTTT",
"TGTGCAGCAAGCTCTGGGGCAAACAACCTCTTCTTT",
"CASSLARASNEKLFF",
"CAASSGANNLFF",
"TRBV7-2",
"None",
"TRBJ1-4",
"TRAV29/DV5",
"TRAJ36",
"TRBC1",
"TRAC",
"True",
"True",
"9.0",
"3.0",
"TRBV7-2",
"TRAV29/DV5",
"None",
"TRBJ1-4",
"TRAJ36",
"TRBC1",
"TRAC",
"TRBV7-2",
"None",
"TRBJ1-4",
"TRAV29/DV5",
"TRAJ36",
"None",
"None",
"TRB + TRA",
"Single pair",
"standard",
"standard"
]
],
"shape": {
"columns": 46,
"rows": 5333
}
},
"text/html": [
"| \n", " | clone_id | \n", "clone_id_by_size | \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", "v_call_VJ | \n", "... | \n", "d_call_abT_VDJ_main | \n", "j_call_abT_VDJ_main | \n", "v_call_abT_VJ_main | \n", "j_call_abT_VJ_main | \n", "isotype | \n", "isotype_status | \n", "locus_status | \n", "chain_status | \n", "rearrangement_status_VDJ | \n", "rearrangement_status_VJ | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AAACCTGAGCGATAGC-1 | \n", "abT_VDJ_119_5_2_VJ_306_2_3 | \n", "422 | \n", "TRB | \n", "TRA | \n", "True | \n", "True | \n", "TRBV6-5 | \n", "None | \n", "TRBJ2-3 | \n", "TRAV23/DV6 | \n", "... | \n", "None | \n", "TRBJ2-3 | \n", "TRAV23/DV6 | \n", "TRAJ22 | \n", "None | \n", "None | \n", "TRB + TRA | \n", "Single pair | \n", "standard | \n", "standard | \n", "
| AAACCTGAGTCACGCC-1 | \n", "abT_VDJ_225_5_1_VJ_1416_1_1 | \n", "5053 | \n", "TRB | \n", "TRA | \n", "True | \n", "True | \n", "TRBV6-2 | \n", "None | \n", "TRBJ2-6 | \n", "TRAV8-6 | \n", "... | \n", "None | \n", "TRBJ2-6 | \n", "TRAV8-6 | \n", "TRAJ8 | \n", "None | \n", "None | \n", "TRB + TRA | \n", "Single pair | \n", "standard | \n", "standard | \n", "
| AAACCTGCACGTCAGC-1 | \n", "abT_VDJ_225_2_1_VJ_211_2_8 | \n", "4081 | \n", "TRB | \n", "TRA | \n", "True | \n", "True | \n", "TRBV6-2 | \n", "None | \n", "TRBJ2-6 | \n", "TRAV1-2 | \n", "... | \n", "None | \n", "TRBJ2-6 | \n", "TRAV1-2 | \n", "TRAJ33 | \n", "None | \n", "None | \n", "TRB + TRA | \n", "Single pair | \n", "standard | \n", "standard | \n", "
| AAACCTGGTCAATACC-1 | \n", "abT_VDJ_282_4_3_VJ_1376_2_1 | \n", "4080 | \n", "TRB | \n", "TRA | \n", "True | \n", "True | \n", "TRBV12-4 | \n", "None | \n", "TRBJ2-7 | \n", "TRAV22 | \n", "... | \n", "None | \n", "TRBJ2-7 | \n", "TRAV22 | \n", "TRAJ4 | \n", "None | \n", "None | \n", "TRB + TRA | \n", "Single pair | \n", "standard | \n", "standard | \n", "
| AAACCTGGTTCGGCAC-1 | \n", "abT_VDJ_214_4_8_VJ_1113_2_1|abT_VDJ_214_4_8_VJ... | \n", "4078|4079 | \n", "TRB | \n", "TRA|TRA | \n", "True | \n", "True|True | \n", "TRBV20-1 | \n", "None | \n", "TRBJ1-1 | \n", "TRAV8-3|TRAV8-2 | \n", "... | \n", "None | \n", "TRBJ1-1 | \n", "TRAV8-3 | \n", "TRAJ21 | \n", "None | \n", "Multi | \n", "TRB + Extra VJ | \n", "Extra 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", "
| TTTGTCATCGCCGTGA-1 | \n", "abT_VDJ_382_1_1_VJ_723_1_1 | \n", "2061 | \n", "TRB | \n", "TRA | \n", "True | \n", "True | \n", "TRBV12-4 | \n", "None | \n", "TRBJ2-3 | \n", "TRAV8-2 | \n", "... | \n", "None | \n", "TRBJ2-3 | \n", "TRAV8-2 | \n", "TRAJ13 | \n", "None | \n", "None | \n", "TRB + TRA | \n", "Single pair | \n", "standard | \n", "standard | \n", "
| TTTGTCATCGTCTGAA-1 | \n", "abT_VDJ_338_3_1_VJ_592_2_1 | \n", "2060 | \n", "TRB | \n", "TRA | \n", "True | \n", "True | \n", "TRBV7-8 | \n", "None | \n", "TRBJ1-3 | \n", "TRAV8-6 | \n", "... | \n", "None | \n", "TRBJ1-3 | \n", "TRAV8-6 | \n", "TRAJ27 | \n", "None | \n", "None | \n", "TRB + TRA | \n", "Single pair | \n", "standard | \n", "standard | \n", "
| TTTGTCATCTACCAGA-1 | \n", "abT_VDJ_502_3_1_VJ_621_3_1 | \n", "2059 | \n", "TRB | \n", "TRA | \n", "True | \n", "True | \n", "TRBV6-6 | \n", "TRBD1 | \n", "TRBJ2-3 | \n", "TRAV8-6 | \n", "... | \n", "TRBD1 | \n", "TRBJ2-3 | \n", "TRAV8-6 | \n", "TRAJ48 | \n", "None | \n", "None | \n", "TRB + TRA | \n", "Single pair | \n", "standard | \n", "standard | \n", "
| TTTGTCATCTCTGAGA-1 | \n", "abT_VDJ_372_5_1_VJ_1420_1_1|abT_VDJ_58_3_1_VJ_... | \n", "2057|2058 | \n", "TRB|TRB | \n", "TRA | \n", "True|True | \n", "True | \n", "TRBV7-2|TRBV11-2 | \n", "None | \n", "TRBJ1-2|TRBJ1-4 | \n", "TRAV3 | \n", "... | \n", "None | \n", "TRBJ1-2 | \n", "TRAV3 | \n", "TRAJ22 | \n", "None|None | \n", "Multi | \n", "Extra VDJ + TRA | \n", "Extra pair | \n", "standard | \n", "standard | \n", "
| TTTGTCATCTTCGAGA-1 | \n", "abT_VDJ_359_1_5_VJ_1561_4_1 | \n", "6080 | \n", "TRB | \n", "TRA | \n", "True | \n", "True | \n", "TRBV2 | \n", "None | \n", "TRBJ1-5 | \n", "TRAV12-1 | \n", "... | \n", "None | \n", "TRBJ1-5 | \n", "TRAV12-1 | \n", "TRAJ9 | \n", "None | \n", "None | \n", "TRB + TRA | \n", "Single pair | \n", "standard | \n", "standard | \n", "
5333 rows × 46 columns
\n", "