Find mean read length of a bam file dataset of reads?
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22 months ago
MobiusT ▴ 10

I am working in a remote linux server and I have a dataset of reads in the file with extension bam extension. How to find its mean read length

bam dataset read gz linux • 1.0k views
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vcfs don't usually contain read length information

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Do not delete posts that have received feedback.

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22 months ago

you can get the mean read length from a bam or a fastq file, not from a VCF.

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Then, How to find from a bam file?

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samtools stats in.bam | grep "average length"

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