Question: Coverage and fragment length
0
gravatar for aaron.agri
3.6 years 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 • 1.5k views
ADD COMMENTlink modified 3.6 years ago by Devon Ryan98k • written 3.6 years ago by aaron.agri0

Is it paired or single end ?

ADD REPLYlink written 3.6 years ago by Carlo Yague5.7k

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

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by cpad011215k
1
gravatar for Devon Ryan
3.6 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

If you have deepTools installed, use bamPEFragmentSize and plotCoverage.

ADD COMMENTlink written 3.6 years ago by Devon Ryan98k
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