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    "# Dandelion for TCR gamma/delta reannotation\n",
    "\n",
    "In Cell Ranger 3.1.0, the VDJ algorithm was changed to favour TCR alpha/beta annotation. Since then, calling gamma/delta chains has become challenging, and 10X support recommends using Cell Ranger 3.0.2 when working with gamma/delta-rich libraries. \n",
    "\n",
    "However, the contigs themselves are still accurately reconstructed, just not annotated correctly. It may be desirable to use a newer Cell Ranger version for access to some previously unavailable run options, like specifying custom enrichment primers. In those cases, the contigs can be reannotated via `dandelion` to yield functional output.\n",
    "\n",
    "Just follow [standard protocol](https://sc-dandelion.readthedocs.io/en/latest/notebooks/Q1-singularity-preprocessing.html) for preparing and running the preprocessing. The parameterisation recommendation is applicable here as well:\n",
    "\n",
    "```bash\n",
    "singularity run -B $PWD /path/to/sc-dandelion_latest.sif dandelion-preprocess \\\n",
    "     --chain TR \\\n",
    "     --file_prefix all \\\n",
    "     --filter_to_high_confidence\n",
    "```"
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