Question: Depth of Coverage - Calculated Per Probe / Bed Region
0
gravatar for jnowacki
6 months ago by
jnowacki40
jnowacki40 wrote:

I'm trying to find out the average depth of coverage per target region in a bed file. I can easily use bedtools -depth to find the depth of coverage at each base, but I'd much rather have it as average coverage per region. The bedtools "-hist" option produces 110 reports on one of my features. I only want 1 number (average coverage) per target region. Any way to do this?

I found threads from a few years ago but wonder if there is anything current. One of the solutions doesn't compile on my Ubuntu server and the bash script gets a "fatal: division by zero attempted"

Depth of coverage for specific target from bam file

depth tool bam bed • 465 views
ADD COMMENTlink modified 6 months ago by Kevin Blighe24k • written 6 months ago by jnowacki40
0
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe24k
USA / Europe / Brazil
Kevin Blighe24k wrote:

Please take a look at my answer here: Compute mean depth coverage for exome data with paired end, overlapping, features I believe that you require BEDTools version > 2.0.

Also some simple code for plotting the profile: Histogram showing overlap between 2 bed files

Kevin

ADD COMMENTlink written 6 months ago by Kevin Blighe24k
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: 700 users visited in the last hour