bedtools command output

cmccabe · 06-18-2015, 10:12 AM

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

WhatsOEver · 06-19-2015, 05:44 AM

Maybe you should have a look at the bedtools website in order to understand what you are doing

cmccabe · 06-19-2015, 06:14 AM

I have read that but still not sure. Thank you

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06-19-2015, 05:44 AM	#2
WhatsOEver Senior Member Location: Germany Join Date: Apr 2012 Posts: 215	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

06-19-2015, 06:14 AM	#3
cmccabe Senior Member Location: chicago Join Date: Jul 2012 Posts: 354	I have read that but still not sure. Thank you