bedtools giving me an error, new program suggestions?

[ninja_help]

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

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

[vivek_]

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]

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!