Question: Coverage and fragment length
0
gravatar for aaron.agri
4 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 • 301 views
ADD COMMENTlink modified 4 months ago by Devon Ryan74k • written 4 months ago by aaron.agri0

Is it paired or single end ?

ADD REPLYlink written 4 months ago by Carlo Yague3.5k

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

ADD REPLYlink modified 4 months ago • written 4 months ago by cpad01123.8k
0
gravatar for Devon Ryan
4 months ago by
Devon Ryan74k
Freiburg, Germany
Devon Ryan74k wrote:

If you have deepTools installed, use bamPEFragmentSize and plotCoverage.

ADD COMMENTlink written 4 months ago by Devon Ryan74k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1262 users visited in the last hour