Question: Coverage and fragment length
0
gravatar for aaron.agri
11 months 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 • 513 views
ADD COMMENTlink modified 11 months ago by Devon Ryan81k • written 11 months ago by aaron.agri0

Is it paired or single end ?

ADD REPLYlink written 11 months ago by Carlo Yague4.1k

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

ADD REPLYlink modified 11 months ago • written 11 months ago by cpad01127.7k
0
gravatar for Devon Ryan
11 months ago by
Devon Ryan81k
Freiburg, Germany
Devon Ryan81k wrote:

If you have deepTools installed, use bamPEFragmentSize and plotCoverage.

ADD COMMENTlink written 11 months ago by Devon Ryan81k
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