Hi, Has any one have problem with converting gff3 to GenePred file using gff3toGenePred from Kent/Ucsc?
Here is my gff3 file. When I use ~/bin/x86_64/gff3ToGenePred nomask_110621N.gff nogffGp, I got empty file without any error message so I don't know what's wrong? I have also tried gtfToGenePred but it was so difficult to get the right Gtf format so at the end I didn't get the right GenePred format. Scaffold1 AUGUSTUS gene 1 2458 0.83 + . ID=aug_v1.1-nomask.00001 Scaffold1 AUGUSTUS transcript 1 2458 0.83 + . ID=aug_v1.1-nomask.00001.t1;Parent=aug_v1.1-nomask.00001 Scaffold1 AUGUSTUS intron 1 425 0.92 + . Parent=aug_v1.1-nomask.00001.t1 Scaffold1 AUGUSTUS intron 519 1483 1 + . Parent=aug_v1.1-nomask.00001.t1 Scaffold1 AUGUSTUS intron 1599 1697 1 + . Parent=aug_v1.1-nomask.00001.t1 Scaffold1 AUGUSTUS intron 1751 2330 0.98 + . Parent=aug_v1.1-nomask.00001.t1 Scaffold1 AUGUSTUS CDS 426 518 0.94 + 2 ID=aug_v1.1-nomask.00001.t1.cds;Parent=aug_v1.1-nomask.00001.t1 Scaffold1 AUGUSTUS exon 426 518 . + . Parent=aug_v1.1-nomask.00001.t1 Scaffold1 AUGUSTUS CDS 1484 1598 1 + 2 ID=aug_v1.1-nomask.00001.t1.cds;Parent=aug_v1.1-nomask.00001.t1 Scaffold1 AUGUSTUS exon 1484 1598 . + . Parent=aug_v1.1-nomask.00001.t1 Scaffold1 AUGUSTUS CDS 1698 1750 1 + 1 ID=aug_v1.1-nomask.00001.t1.cds;Parent=aug_v1.1-nomask.00001.t1 Scaffold1 AUGUSTUS exon 1698 1750 . + . Parent=aug_v1.1-nomask.00001.t1 Scaffold1 AUGUSTUS CDS 2331 2365 0.97 + 2 ID=aug_v1.1-nomask.00001.t1.cds;Parent=aug_v1.1-nomask.00001.t1 Scaffold1 AUGUSTUS exon 2331 2458 . + . Parent=aug_v1.1-nomask.00001.t1 Scaffold1 AUGUSTUS stop_codon 2363 2365 . + 0 Parent=aug_v1.1-nomask.00001.t1 Scaffold1 AUGUSTUS transcription_end_site 2458 2458 . + . Parent=aug_v1.1-nomask.00001.t1 Any suggestion will be great. Best regards, Sutada _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
