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.
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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