11.3. Create BED from GTF

For generating a BED file from a GTF.

The genes.gtf file should be copied to the genome directory.

localhost:~> mkdir genome
localhost:~> cd genome
localhost:~> cwl-runner --no-container https://github.com/ncbi/cwl-ngs-workflows-cbb/blob/master/workflows/UCSC/gtftobed.cwl --gtf genes.gtf
localhost:~> tree
.
├── genes.bed
├── genes.genePred
└── genome.gtf

0 directory, 3 files

Here the files genes.bed and genes.genePred are created from the workflow.