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Old 08-13-2015, 07:53 AM   #1
ninja_help
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Location: West Coast

Join Date: Aug 2015
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Default bedtools giving me an error, new program suggestions?

Hi all

Recently I started using bedtools as a way of analyzing a genome, it was working fantastically. But I ran into an error which is making me look into other methods of analyzing a genome (other than writing my own script, but alas it might come down to that )

The error I encounter is the following

Quote:
Start was greater than end.
This occurred because my coordinates for several positions in the genome were going from say position 60 to 40 as a result of an analysis I ran using RepeatMasker.

My question is there a program that would take and not give me an error. Or do I have to come to my own and write my own script ?

Cheers
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Old 08-13-2015, 07:59 AM   #2
vivek_
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That error is very logical if you want the tool to work on bed files. You could flip the coordinates and add a 4th column indicating +/- in the BED file to preserve orientation for such cases before using BEDtools.
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Old 08-13-2015, 08:08 AM   #3
ninja_help
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Quote:
Originally Posted by vivek_ View Post
That error is very logical if you want the tool to work on bed files. You could flip the coordinates and add a 4th column indicating +/- in the BED file to preserve orientation for such cases before using BEDtools.
ahh I tried that on a much shorted example but didnt flip the coordinates. Thanks!
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