How to retrieve the number of reads mapped for each chromosome in the BAM file of methylation data

I want to retrieve the number of reads mapped for each chromosome in the BAM file of methylation data. Anyone know how I can get this? Thank you in advance.

bam methylation mapped read

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updated 2.8 years ago by GenoMax

• written 2.8 years ago by sata72 •

1 answer

You can do this-

samtools idxstats your_data.bam | cut -f 1,3

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written 2.8 years ago by bk11 •

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