I have some issues with bedtools genomecov. My goal is to produce bedgraph outputs from bed files using bedtools genomecov. With bed files as input, it requires a genome file. I got it from uscs table browser. It is a tab-delimitated file with 3 columns : chr / size / filename I removed the third one and the first line that contains the names of the column but I get an error message from bedtools :
". Exiting...illegal number" 32079331
32079331 is the size of the first chromosome When I add an empty column using tabulation after 32079331, then it recognises the first chromosome but not the following one. So I added an empty column after each chromosome. When It comes to the last one however, I get another error message :
Unexpected file format. Please use tab-delimited BED, GFF, or VSF. Perhaps you have non-intger starts or ends.
I changed the format from .genome to .bed but it does not change anything.. I don't understand. I hope someone can help. Thank you very much in advance!