I am using gffread (v0.12.7) to extract transcript sequences based on a stringtie merged gtf file. After looking through gffread's usage, I want to use -w to extract sequences of exons, and -x to extract cds.
My command are as following:
gffread -w exon.fa -x cds.fa -g genome stringtie_merged.gtf
The result exon.fa seems fine, but cds.fa is an empty file. I am wondering is there anything I can do about this.
Thanks a lot, Liyong