Hi Sutada, We've looked into the issue and found that you are using "transcript" rather than "mRNA" for the mRNA features. You will need to correct this. If you have further questions, please contact the mailing list: [email protected].
Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: sutada Mungpakdee <[email protected]> Date: Wed, Nov 9, 2011 at 5:23 PM Subject: [Genome] gff3 to GenePred To: [email protected] Hi, I have question regarding to convert gff3 file to GenePred. I have download gff3toGenePred from kent/x86_64. Here is my gff3 file and I got the empty gp file. ##gff-version 3 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 Scaffold1 AUGUSTUS gene 3276 29853 0.02 + . ID=aug_v1.1-nomask.00002 Do you have any idea what went wrong? Any suggestion will be great. Best regards, Sutada _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
