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

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.

cell-ranger samtools bam cell-barcode

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updated 3.1 years ago by Ram

• written 4.2 years ago by tien •

1 answer

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

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written 4.2 years ago by GenoMax

Oh yesss. Thanks a lot.

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written 4.2 years ago by tien •

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