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Old 06-18-2015, 06:54 AM   #1
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Location: chicago

Join Date: Jul 2012
Posts: 354
Default average coverage in target regions

I am trying to get the _X coverage in a bam file for target regions in a bed.

find *bam | parallel 'bedtools coverage -hist -abam IonXpress_009_150603.bam -b epilepsy70_medex.bed | grep ^all > output.bam.hist.txt' > all.txt
The files are too large to attach but after the -abam is the bam file to use, after the -b is the terget bed to use with the baits, after the grep^all is the bedTools coverage output and the > all.txt are the results. Is there something missing? Thank you .

Maybe this:
coverageBed -abam IonXpress_009_150603.bam -b epilepsy70_medex.bed -counts > count.txt

Last edited by cmccabe; 06-18-2015 at 07:23 AM. Reason: added code
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