<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">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.<div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 31, 2016, at 4:51 AM, Jacques Dainat <<a href="mailto:jacques.dainat@bils.se" class="">jacques.dainat@bils.se</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hello,</div><div class=""><br class=""></div><div class="">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.</div><div class="">This time I used Stringtie output to feed Maker, but I don’t have any gene model predicted using the est2genome parameter.</div><div class=""><br class=""></div><div class="">Any explanation ? Is it due to the gff3 format differences between these two file ?</div><div class=""><br class=""></div><div class="">Cufflinks output example:</div><div class=""><div style="margin: 0px; font-size: 11px; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(44, 103, 200);" class="">Pnalgiovense_4592 Cufflinks match 363 977 17.844829 - . ID=1:s3_c1_r1.4.2;Name=1:s3_c1_r1.4.2;</div><div style="margin: 0px; font-size: 11px; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(44, 103, 200);" class="">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 +;</div><div style="margin: 0px; font-size: 11px; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(44, 103, 200);" class="">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 +;</div></div><div class=""><br class=""></div><div class="">Stringtie output example:</div><div class=""><div style="margin: 0px; font-size: 11px; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(44, 103, 200);" class="">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</div><div style="margin: 0px; font-size: 11px; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(44, 103, 200);" class="">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</div><div style="margin: 0px; font-size: 11px; font-family: Menlo; color: rgb(255, 255, 255); background-color: rgb(44, 103, 200);" class="">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</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">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 ?</div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""><br class=""></div><br class=""><div apple-content-edited="true" class="">
<div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Jacques Dainat, PhD</div><div class="">NBIS (National Bioinformatics Infrastructure Sweden)</div><div class="">Genome Annotation Service</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><u class="">Address:</u><span class="Apple-converted-space"> </span>(room E10:4204 - last floor)</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Uppsala University, BMC<br class="">Department of Medical Biochemistry Microbiology, Genomics</div>Husargatan 3, box 582</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">S-75123 Uppsala Sweden</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Phone: 01 84 71 46 25</div></div></div></div></div></div></div></div></div>
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