Question: Getting coordinates with bad deep/coverage from a bam file
0
gravatar for Enka
4.1 years ago by
Enka10
Enka10 wrote:

I received .bam files for bacterial genomes sequenced by SOLiD and mapped to a reference genome by bioscope. I have found that some areas have really few reads aligned (as few as 2). I would like to know if there is a way to get the coordinates of the regions that have a deep (or coverage) below certain threeshold, so I can assess how big is this problem for each aligment.

igv bam resequencing solid • 1.1k views
ADD COMMENTlink modified 4.1 years ago by geek_y10k • written 4.1 years ago by Enka10
1
gravatar for geek_y
4.1 years ago by
geek_y10k
Barcelona
geek_y10k wrote:

A: How get intervals of low coverage from a genome sequence?

ADD COMMENTlink written 4.1 years ago by geek_y10k

My bad. Thanks a lot.

ADD REPLYlink written 4.1 years ago by Enka10
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: 1677 users visited in the last hour