Quantifying "unmapped" reads

10XGenomics / scHLAcount

Count HLA alleles in single-cell RNA-seq data

MIT License

58 stars 12 forks source link

Quantifying "unmapped" reads #19

Open joycekang opened 3 years ago

joycekang commented 3 years ago

Hello! Thanks for making such a great tool.

I was wondering if it is possible to add the unmapped reads from the bam file in the quantification step? I see that currently it is an option for the genotyping step but not the quantification step. Thanks!