Coverage and fragment length

Question

[aaron.agri]

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

[Carlo Yague]

Is it paired or single end ?

[cpad0112]

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

Answer 1

[Devon Ryan]

If you have deepTools installed, use bamPEFragmentSize and plotCoverage.