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MarioniLab / DropletUtils

Clone of the Bioconductor repository for the DropletUtils package.
https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html
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rowRanges Needs to be Manually Filled In #106

Closed DarioS closed 8 months ago

DarioS commented 8 months ago

Could read10xCounts offer the convenience of recording row ranges to remove a step before addPerCellQCMetrics for mitochondrial content? A new parameter e.g. GTFpath could allow the user could specify e.g. "refdata-gex-mm10-2020-A/genes/genes.gtf".

LTLA commented 8 months ago

IMO this seems out of scope for read10xCounts. Unless the GTF is part of the CellRanger output directory (and I'm pretty sure it isn't), it shouldn't be read10xCounts's job to pull in that information.

But surely it's a one-liner that isn't too hard for users to write? Something like:

rowRanges(sce) <- rtracklayer::import("my.gtf")[rownames(sce)]
DarioS commented 8 months ago

It is not part of the output directory, but in their standard GZip reference genome in genes folder as shown above.