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powellgenomicslab / DropletQC

Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data
https://powellgenomicslab.github.io/DropletQC/
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Taking output from cell ranger multi #11

Open yjqiu opened 10 months ago

yjqiu commented 10 months ago

Hi,

I am analyzing 10X multi-data with cell ranger multi. It has different output structures compared to cellranger count. Is there a way to support output from multi? Thanks a lot!

WalterMuskovic commented 6 months ago

Hi @yjqiu, to calculate the nuclear fraction all you need are the BAM file and barcodes. Since the directory structure and file names are different for cell ranger multi compared to cell ranger count, you can specify the path to the barcode and bam files with the barcodes and bam arguments to the nuclear_fraction_tags() function. See ?nuclear_fraction_tags for full details. The bam file sample_alignments.bam will be in the count/ directory.

yjqiu commented 6 months ago

Thanks! It works! But it would be nice to have a high level wrapper that point to multi dir directly as count.