Question: 'BEDcov' and 'compute depth and breadth'
0
gravatar for c.zijlstra
22 months ago by
c.zijlstra0
c.zijlstra0 wrote:

In galaxy I used boht the SAMtool bedcov and the bedtool 'Compute both depth and breath' to calculate the read depth in my samples. However, I get quite different numbers for depth with the two tools (depth in bedcov always higher), How can this be explained??

kind regards, carla

bedtools bed coverage samtools bam • 979 views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 22 months ago by c.zijlstra0
0
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Samtools BedCov counts read that completely overlap the target intervals. BedTools Compute both depth and breath does a bit more - it counts partial overlaps, too.

The tool forms have more details and links to the manuals for the exact differences in the algorithms.

Best, Jen, Galaxy team

ADD COMMENTlink modified 22 months ago • written 22 months ago by Jennifer Hillman Jackson25k
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