The getIntrons.sh uses gencode GTF annotation files to create an intronic GTF file which is usually unavailable. Running the script is simple. First install the following:
- Install BEDops
- Install bedtools
- Annotation files, gencode human or any annotation in GTF format that contains exon and gene features
Once installed, edit the GENE_ANNOT_FILE variable in getIntrons.sh such that it points to where your annotations are. Then run:
./getIntrons.sh
Once finished, you should see introns.gtf in your directory.