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BEDTools: Unexpected file format. Please use tab-delimited BED, GFF, or VCF.

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  • #16
    In the future, you really need to include the exact command line you are using.

    I'm pretty sure the problem is this: BED format is valid with only three columns of data, but I think coverageBed needs four columns of data; I think it wants a column for direction.

    Try adding a fourth column of all pluses.

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    • #17
      @swbarnes2, does the 4th column need to be the direction or can it be gene names as well ? I have a .BED file that has some annotation information in the 4th column. Would that still be okay ?

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