Question: bedtools genomecov .genome file usage
4
gravatar for kaston
5.7 years ago by
kaston40
Canada
kaston40 wrote:

I'm using the bedtools genomecov command to find coverage stats for a human genome alignment:

bedtools genomecov -ibam foo.bam

The bedtools documentation (http://bedtools.readthedocs.org/en/latest/content/overview.html) says that you need to specify a .genome file so the tool knows how big the chromosomes are using the "-g filename.genome" option.  I havenèt done this, but the command still works.

How does it know what the chromosome sizes are?  Is it pointing to a .genome file somewhere in the system that I'm not aware of or is this simply not necessary contrary to the documentation?

Thanks.

 

genomecov bedtools • 4.8k views
ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by kaston40
4
gravatar for Aaronquinlan
5.7 years ago by
Aaronquinlan11k
United States
Aaronquinlan11k wrote:

With a BAM file, this is unnecssary. Sorry for the confusing docs.

ADD COMMENTlink written 5.7 years ago by Aaronquinlan11k
0
gravatar for kaston
5.7 years ago by
kaston40
Canada
kaston40 wrote:

thanks for the prompt reply!

ADD COMMENTlink written 5.7 years ago by kaston40

Please add your reply to a comment to the answer.

ADD REPLYlink written 5.2 years ago by SmallChess540
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: 1737 users visited in the last hour