[swbarnes2]

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.

[aditisk]

@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 ?

[Michael.Ante]

Dear aditisk,

you may have a look here.
The 4th column is reserved for the name, the 5th is the score, and the 6th is the strand.

[Michael.Ante]

Hi aditisk,
please see more information here.
The 4th column is reserved for the name, the 5th one for the score, and the strand is 6th column.
Cheers,
Michael

[Michael.Ante]

Hi aditisk,

you might have a look at the bed-definition (e.g. here).
The 4th column is reserved for the name (e.g. klk5, my_feature, or exon), the fifth for the score, and the strand is written in the 6th column.

Cheers,

Michael