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