https://bioinformaticsonline.com/snippets/view/42026/bash-script-to-extract-intronic-fragments? https://bioinformaticsonline.com/snippets/view/42026/bash-script-to-extract-intronic-fragments Sat, 08 Aug 2020 20:07:46 -0500 https://bioinformaticsonline.com/snippets/view/42026/bash-script-to-extract-intronic-fragments #To obtain introns, we simply need the gene and exonic coordinates; #by subtracting the exonic regions from the genic region, we have the intronic region. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {print $1,$4-1,$5}' | bedtools sort | bedtools subtract -a stdin -b my_exon.bed.gz | gzip > my_intron.bed.gz]]> BioStar