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Coverage and fragment length

I have bam file aligned with the reference genome, need to know how to know the average fragment length and coverage?

alignment

Is it paired or single end ?

from SAM, TLEN gives out average fragment size and try CollectInsertSizeMetrics from PICARD tools and for coverage, use samtools.

1 answer

If you have deepTools installed, use bamPEFragmentSize and plotCoverage.

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