[maker-devel] est_gff input does not provide any gene model

[Carson Holt]

Evidence such as est_gff has to follow the alignment format used by GFF3 (i.e. match/match_part) whereas you are providing gene models (i.e. gene/mRNA/exon/CDS). Note that match/match_part are two level features whereas gene models are 3 levels. You need to reformat to match/match_part.

—Carson


> On Oct 31, 2016, at 4:51 AM, Jacques Dainat <jacques.dainat at bils.se> wrote:
> 
> Hello,
> 
> I’m using usually Cufflinks output to feed Maker through the est_gff parameter, combined with the est2genome=1 parameter I get the wanted output.
> This time I used Stringtie output to feed Maker, but I don’t have any gene model predicted using the est2genome parameter.
> 
> Any explanation ? Is it due to the gff3 format differences between these two file ?
> 
> Cufflinks output example:
> Pnalgiovense_4592      Cufflinks       match   363     977     17.844829       -       .       ID=1:s3_c1_r1.4.2;Name=1:s3_c1_r1.4.2;
> Pnalgiovense_4592      Cufflinks       match_part      363     666     17.844829       -       .       ID=1:s3_c1_r1.4.2:exon-1;Name=1:s3_c1_r1.4.2;Parent=1:s3_c1_r1.4.2;Target=1:s3_c1_r1.4.2 1 304 +;
> Pnalgiovense_4592      Cufflinks       match_part      743     977     17.844829       -       .       ID=1:s3_c1_r1.4.2:exon-2;Name=1:s3_c1_r1.4.2;Parent=1:s3_c1_r1.4.2;Target=1:s3_c1_r1.4.2 305 539 +;
> 
> Stringtie output example:
> Pnalgiovense_112      StringTie       gene    20      1256    1000    +       .       ID=HtMm_All.12253;cov=8.028295;fPKM=1.214491;gene_id=HtMm_All.12253;tPM=2.706611;transcript_id=HtMm_All.12253.1
> Pnalgiovense_112      StringTie       mRNA    20      1256    1000    +       .       ID=HtMm_All.12253.1;Parent=HtMm_All.12253;cov=8.028295;fPKM=1.214491;gene_id=HtMm_All.12253;tPM=2.706611;transcript_id=HtMm_All.12253.1
> Pnalgiovense_112      StringTie       exon    20      1256    1000    +       .       ID=HtMm_All.12253.1-exon-1;Parent=HtMm_All.12253.1;cov=8.028295;exon_number=1;gene_id=HtMm_All.12253;transcript_id=HtMm_All.12253.1
> 
> 
> If it’s the Stringtie output that is problematic how can I fix it ? Removing gene, changing mRNA by match and exons by match_part is enough ?
> 
> Best regards,
> 
> 
> Jacques Dainat, PhD
> NBIS (National Bioinformatics Infrastructure Sweden)
> Genome Annotation Service
> 
> Address: (room E10:4204 - last floor)
> Uppsala University, BMC
> Department of Medical Biochemistry Microbiology, Genomics
> Husargatan 3, box 582
> S-75123 Uppsala Sweden
> Phone: 01 84 71 46 25
> 
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