Add support for non- Cell Ranger SAM tags #48
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This was referenced Apr 15, 2024
Cell Ranger uses `CB` SAM tags for the cell barcode and `UB` SAM tags for the UMI but other scRNA-seq pipelines use different tags (*e.g.* `XC` and `XM`). This commit introduces the `CELL_TAG` and `UMI_TAG` environment variables to override the Cell Ranger style defaults. Note: For Demuxalot, this requires v.0.4.1 or higher.
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@drneavin: I rebased this on your v3.0.0 branch and resolved all conflicts. |
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Cell Ranger uses
CBSAM tags for the cell barcode andUBSAM tags for the UMI but other scRNA-seq pipelines use different tags (e.g.XCandXM).This commit introduces the
CELL_TAGandUMI_TAGenvironment variables to override the Cell Ranger style defaults.Note: For Demuxalot, this requires upstream changes
suggested in the following PR: arogozhnikov/demuxalot#26introduced inv.0.4.1. Therefore, itnot onlydoesitdependon that one to be merged (which should happen 'soon'), but alsoon updating the Demuxalot version bundled in the Demuxafy Singularity Image to one including those upstream changes (>= v.0.4.1).Thus, this PR must not be merged before #46 (or, IMHO better: #47) is merged as well.@drneavin: Merging this and releasing a new version would enable me to use Demuxafy on a lot of data we already have analysed without having to re-analyse them all from scratch with Cell Ranger. I have tested those changes locally using the (reduced) test dataset as well as one of my non- Cell Ranger datasets.