Script for calculating the average distribution of tags per gene from ChIP-seq??

Giles · 08-30-2011, 08:16 AM

I seem to recall a script for calculating the average distribution of tags per gene from a ChIP-seq experiment. I thought this was a BEDTools script, but don't see it in there. I also couldn't find it in SAMTools. Does anyone know of such a publically available script?

dariober · 09-12-2011, 03:25 AM

Quote:

Originally Posted by Giles

I seem to recall a script for calculating the average distribution of tags per gene from a ChIP-seq experiment. I thought this was a BEDTools script, but don't see it in there. I also couldn't find it in SAMTools. Does anyone know of such a publically available script?

Maybe coverageBEd in bedtools gets closer to what you want?

Code:

coverageBed -abam myreads.bam -b mygenes.gft -hist

Dario

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08-30-2011, 08:16 AM	#1
Giles Member Location: Birmingham, Al Join Date: Feb 2010 Posts: 39	Script for calculating the average distribution of tags per gene from ChIP-seq?? I seem to recall a script for calculating the average distribution of tags per gene from a ChIP-seq experiment. I thought this was a BEDTools script, but don't see it in there. I also couldn't find it in SAMTools. Does anyone know of such a publically available script?