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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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Filtering cells before or after cellsnp-lite #68

Closed haigdjambazian closed 1 year ago

haigdjambazian commented 1 year ago

If I wanted to only consider real cells is there a way to filter cells that have too low read counts? I see how I could filter the input reads or bam myself before cellsnp-lite but I was wondering what you think. Can vireo filter cells out before running? Thanks.

hxj5 commented 1 year ago

Hi, cellsnp-lite or vireo can not filter cells with low read counts. This task is more like "cell calling". You may use cell barcodes stored in cellranger folder filtered_gene_bc_matrices, or filter cells based on the UMI/read counts generated from the bam file.