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I am trying to use the geneBody_coverage.py script from RSeQC, which requires a tab-separated 12-column .bed file as a reference. To do so, I used gff2bed script to convert a .gff3 file from Ensembl to a .bed format. When I run it, I only get errors informing me the file is not in 12-column format. A colleague told me he also tried using gff2bed on Ensembl files and the format was incorrect for him as well. Are there any solutions to this?

I have tried the same thing with a different .gff3 Ensembl file with the same result. I've also tried gtf2bed with the same result.

Dysnomia
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1 Answers1

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I figured something out. I used gff3ToGenePred followed by genePredToBed tools from UCSC utilities. This outputs a 12-column .bed.

Dysnomia
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