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

[Jacques Dainat]

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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