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Old 06-18-2015, 09:12 AM   #1
cmccabe
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Location: chicago

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Default bedtools command output

Not sure what the output of this command means, but I am trying to get the average coverage per bait in a bed file. Thank you .

Code:
 coverageBed -hist -abam IonXpress_009_150603.bam -b epilepsy70_medex.bed | grep ^all > output.hist.all.txt
Code:
all	0	188	195018	0.0009640
all	1	148	195018	0.0007589
all	2	175	195018	0.0008974
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File Type: gz output.hist.all.txt.tar.gz (6.3 KB, 0 views)
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Old 06-19-2015, 04:44 AM   #2
WhatsOEver
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Maybe you should have a look at the bedtools website in order to understand what you are doing
http://bedtools.readthedocs.org/en/l.../coverage.html
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Old 06-19-2015, 05:14 AM   #3
cmccabe
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I have read that but still not sure. Thank you
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