<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=""><div class="">Thank you for the quick confirmation !</div><div class=""><br class=""></div><div class="">Just for clarification, what I provided to Maker was a correct gff3 file that indeed contain gene,mRNA,exon types but does not contain any CDS.</div><div class=""><br class=""></div><div class="">I haven’t seen any information about the particular gff3 feature types expected for the est_gff files supplied. I think you should communicate more about it (within the maker_opt.ctl ?).</div><div class="">It would be nice to stop the pipeline if the file provided contains no information. (When the file provided doesn’t exits too. The warning is not obvious to catch when launching on a cluster...)</div><div class=""><br class=""></div><div class="">A last question. do the scores from the score column are used by MAKER from the est_gff file ?</div><div class=""><br class=""></div><div apple-content-edited="true" class="">
<div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: 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="color: rgb(0, 0, 0); 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="color: rgb(0, 0, 0); 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="color: rgb(0, 0, 0); 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="color: rgb(0, 0, 0); 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="color: rgb(0, 0, 0); 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="color: rgb(0, 0, 0); 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="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: 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 </div></div></div></div></div></div></div></div></div></div>
<br class=""><div><blockquote type="cite" class=""><div class="">On 01 Nov 2016, at 04:24, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</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="">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 class=""><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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