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-   -   bedtools giving me an error, new program suggestions? (http://seqanswers.com/forums/showthread.php?t=61963)

ninja_help 08-13-2015 07:53 AM

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 :rolleyes: )

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 :D?

Cheers

vivek_ 08-13-2015 07:59 AM

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.

ninja_help 08-13-2015 08:08 AM

Quote:

Originally Posted by vivek_ (Post 179063)
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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