How to convert GFF3 to BED12?


I am following the Reference based transcriptomics workflow and I have encountered a problem. I am trying to get gene body coverage. But this requires a BED12 format. There is a conversion tool for GTF to BED12 but not one for GFF3 to BED12 (that I know of)?

Any advice?

Hi @reltubycul

GTF annotation tends to work better than GFF3 with most tools. If the source has that type of annotation, the conversion will work better. Depending on the source or reference genome, BED12 data might also be available directly.

But, you can try this tool: gffread Filters and/or converts GFF3/GTF2 records. It might only produce a BED6… it was just updated recently and some of the tests I ran still produced odd results for certain use cases.

Please post back what your reference genome is and where you sourced it (if external from Galaxy) should that tool not create a true BED12, and we can try to help more.

Also please post back a link to the tutorial you are following just to confirm. That one has a few different versions at the GTN site, plus other external sites have cloned it. We want to be all reviewing the same analysis content – or can point you to a better version if needed. The tutorial itself would come with “ready” data inputs – but I’m guessing you are using it as a template with your own data.