AWK script for conversion of GFF files to GTF.
USAGE:
awk -f gff2gtf.awk FILE.gff > FILE.gtf
Works with those operating systems that have AWK interpreter. The script relies on the order of records. Ordering is not required for GFF by the specification, but usually records are ordered.
For RSEM:
awk -f gff2gtf-strict.awk FILE.gff > FILE.gtf grep -Ev "\sgene\s" FILE.gtf > rsem-ready.gtf
Tags: NGS, next-generation sequencing, genetics, fasta, DNA, RNA, alignment, genome markup.