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  • ninja_help
    replied
    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!

    Leave a comment:


  • vivek_
    replied
    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.

    Leave a comment:


  • 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

    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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