> Hi, > > Does anyone has this problem when convert gff3 to GenePred? > > When the program convert gff3 to GenePred, the position of exons were > changed and gave frameshift. As I would like to annotate snp > (synonymous/non-synonymous for frameshift SNP) and another software will > count number of BPs from coding start to coding end and then divided by 3. > With exon position generated by gff3toGenePred give the total bp not equal to > number of codon, have one/two residues more. > > Here is gff3 file, > > > Scaffold17 AUGUSTUS gene 1 2885 0.28 - . > ID=aug_v1.1-nomask.01791 > Scaffold17 AUGUSTUS transcript 1 2885 0.28 - > . ID=aug_v1.1-nomask.01791.t1;Parent=aug_v1.1-nomask.01791 > Scaffold17 AUGUSTUS intron 45 470 1 - . > Parent=aug_v1.1-nomask.01791.t1 > Scaffold17 AUGUSTUS intron 552 1459 1 - . > Parent=aug_v1.1-nomask.01791.t1 > Scaffold17 AUGUSTUS CDS 1 44 1 - 0 > ID=aug_v1.1-nomask.01791.t1.cds;Parent=aug_v1.1-nomask.01791.t1 > Scaffold17 AUGUSTUS exon 1 44 . - . > Parent=aug_v1.1-nomask.01791.t1 > Scaffold17 AUGUSTUS CDS 471 551 1 - 0 > ID=aug_v1.1-nomask.01791.t1.cds;Parent=aug_v1.1-nomask.01791.t1 > Scaffold17 AUGUSTUS exon 471 551 . - . > Parent=aug_v1.1-nomask.01791.t1 > Scaffold17 AUGUSTUS CDS 1460 1477 1 - 0 > ID=aug_v1.1-nomask.01791.t1.cds;Parent=aug_v1.1-nomask.01791.t1 > Scaffold17 AUGUSTUS exon 1460 1489 . - . > Parent=aug_v1.1-nomask.01791.t1 > Scaffold17 AUGUSTUS start_codon 1475 1477 . - > 0 Parent=aug_v1.1-nomask.01791.t1 > Scaffold17 AUGUSTUS exon 2011 2086 . - . > Parent=aug_v1.1-nomask.01791.t1 > Scaffold17 AUGUSTUS exon 2377 2451 . - . > Parent=aug_v1.1-nomask.01791.t1 > Scaffold17 AUGUSTUS exon 2776 2885 . - . > Parent=aug_v1.1-nomask.01791.t1 > Scaffold17 AUGUSTUS transcription_start_site 2885 2885 > . - . Parent=aug_v1.1-nomask.01791.t1 > > Scaffold375 AUGUSTUS gene 1 605 0.1 - . > ID=aug_v1.1-nomask.15578 > Scaffold375 AUGUSTUS transcript 1 605 0.1 - > . ID=aug_v1.1-nomask.15578.t1;Parent=aug_v1.1-nomask.15578 > Scaffold375 AUGUSTUS intron 77 373 0.94 - . > Parent=aug_v1.1-nomask.15578.t1 > Scaffold375 AUGUSTUS CDS 1 76 0.91 - 2 > ID=aug_v1.1-nomask.15578.t1.cds;Parent=aug_v1.1-nomask.15578.t1 > Scaffold375 AUGUSTUS exon 1 76 . - . > Parent=aug_v1.1-nomask.15578.t1 > Scaffold375 AUGUSTUS CDS 374 500 0.6 - 0 > ID=aug_v1.1-nomask.15578.t1.cds;Parent=aug_v1.1-nomask.15578.t1 > Scaffold375 AUGUSTUS exon 374 605 . - . > Parent=aug_v1.1-nomask.15578.t1 > Scaffold375 AUGUSTUS start_codon 498 500 . - > 0 Parent=aug_v1.1-nomask.15578.t1 > Scaffold375 AUGUSTUS transcription_start_site 605 605 > . - . Parent=aug_v1.1-nomask.15578.t1 > > > Here is GenePred I got from this gene. > aug_v1.1-nomask.01791.t1 Scaffold17 - 0 2885 0 > 1477 6 0,470,1459,2010,2376,2775, 44,551,1489,2086,2451,2885, > aug_v1.1-nomask.01791 > aug_v1.1-nomask.15578.t1 Scaffold375 - 0 605 0 > 500 2 0,373, 76,605, aug_v1.1-nomask.15578 > > For aug_v1.1-nomask.15578.t1 mRNA lenght = 76+127 = 203 bp which is have 2bp > extra. It should be 201 bp. The first position of the first exon should be 2 > not 0 then the total length = 74+127=201 bp = 67 codons. Do you have any > suggestion? I don't know how to fix the file as almost all genes are > frameshifted. > > Best regards, > Sutada
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