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Old 08-30-2011, 08:16 AM   #1
Giles
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Default 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?
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Old 09-12-2011, 03:25 AM   #2
dariober
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Quote:
Originally Posted by Giles View Post
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
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