In theory, the only way I could see it taking that long is if you have a BED feature for every single base in your genome for the -b file.
chr10 129993255
chr11 121843856
chr12 121257530
chr13 120284312
chr14 125194864
On Fri, Feb 26, 2010 at 10:24 PM, Pratap, Abhishek <APr...@som.umaryland.edu <x-msg://35/APr...@som.umaryland.edu> > wrote:
Hi Aaron
I tried genomeCoverage anyhow. What it gives me is a binned data which is expected. In my case I just need the total coverage xx/chromosome. I know this could be easily calculated by counting reads mapped per chromosome but just wondering if this method exists in BEDtools.
-A
Thanks for the detailing the issue Aaron. It would be actually nice to have coveragebed work on long features but for now I can just grep per chr to calculate rough coverage stats which should suffice.
Thanks!
-Abhi