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Old 06-17-2015, 01:17 PM   #1
cmccabe
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Location: chicago

Join Date: Jul 2012
Posts: 354
Default bedTools 2.20.1 coverageBed [solved]

The output of the bedTools command:

Code:
coverageBed -hist -d -abam IonXpress_001.bam -b LCH_IDT > output.bam.hist.txt
resulted in output like below (output 1 - 6 fields)

output 1
Code:
chr12	112884064	112884217	chr12:112884064-112884217
	1	141
chr12	112884064	112884217	chr12:112884064-112884217
	2	140
and now the same bedTools command outputs (5 fields):

Code:
chr1	40539722	40539865	1	159
chr1	40539722	40539865	2	161
Did something change or is there an option I am forgetting to use? Thank you

Last edited by cmccabe; 06-18-2015 at 07:11 AM.
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Old 06-18-2015, 07:10 AM   #2
cmccabe
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Join Date: Jul 2012
Posts: 354
Default

Forgot to concatenate a line in the bed, its working now. Thank you .
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