Hi, I'm trying to get differential splicing information from some RNA reads using leafcutter. My annotation file is in gff3 format but leafcutter needs a gtf file. I tried converting it using gff read. I get this error message and don't really know what it means:
Error parsing target start coordinate from GFF line: PGA_scaffold23__176_contigs__length_16134482 repeatmasker match 11978391 11978406 13 + . ID=PGA_scaffold23__176_contigs__length_16134482:hit:3923908:126.96.36.199;Name=species:GA-rich|genus:Low_complexity;Target=species:GA-rich|genus:Low_complexity -2 79 +
I hope someone can help me with this.