Count number of unique cell barcode (CB) in bam file

Question

[tien]

Hello all,

I'm having a BAM file from cell ranger and I just sample 1% reads from that file by using samtools --subsample. After sampling, I want to check the number of barcode (CB) and feature (gene_id) in newly created file. Is this possible to do it with samtools or any other tools?

Thanks for your help.

Answer 1

[GenoMax]

This tutorial from 10x will help: https://www.10xgenomics.com/resources/analysis-guides/tutorial-navigating-10x-barcoded-bam-files

[tien]

Oh yesss. Thanks a lot.