Question: Coverage and fragment length
0
gravatar for aaron.agri
11 weeks ago by
aaron.agri0
aaron.agri0 wrote:

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

alignment • 250 views
ADD COMMENTlink modified 11 weeks ago by Devon Ryan71k • written 11 weeks ago by aaron.agri0

Is it paired or single end ?

ADD REPLYlink written 11 weeks ago by Carlo Yague3.2k

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

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by cpad01122.3k
0
gravatar for Devon Ryan
11 weeks ago by
Devon Ryan71k
Freiburg, Germany
Devon Ryan71k wrote:

If you have deepTools installed, use bamPEFragmentSize and plotCoverage.

ADD COMMENTlink written 11 weeks ago by Devon Ryan71k
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