Source of bed file

Question

[Arindam Ghosh]

I am using Homo_sapiens.GRCh38.84.gtf from ENSEMBL for mapping. For post alignment QC using RseQC I need bed file. From where can I get one? I tried using BEDOps but the gtf file doesnot match with the format gtf2bed file uses.

Answer 1

[Devon Ryan]

It's expecting a BED12 file. Here's the rule I use in my Makefile to do the gtf to bed12 conversion:

%.bed: %.gtf
        awk '{if ($$3 != "gene") print $$0;}' $< \
        | grep -v "^#" \
        | /package/UCSCtools/gtfToGenePred /dev/stdin /dev/stdout \
        | /package/UCSCtools/genePredToBed stdin $@

gtfToGenePred and genePredToBed can be downloaded from UCSC. The removal of gene entries are due to them breaking these tools (likewise, you have to remove any comment lines).