Question: bedtools genomecov .genome file usage
3
gravatar for kaston
4.1 years ago by
kaston30
Canada
kaston30 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 • 3.2k views
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by kaston30
4
gravatar for Aaronquinlan
4.1 years ago by
Aaronquinlan10k
United States
Aaronquinlan10k wrote:

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

ADD COMMENTlink written 4.1 years ago by Aaronquinlan10k
0
gravatar for kaston
4.1 years ago by
kaston30
Canada
kaston30 wrote:

thanks for the prompt reply!

ADD COMMENTlink written 4.1 years ago by kaston30

Please add your reply to a comment to the answer.

ADD REPLYlink written 3.6 years ago by SmallChess480
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