<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>One thing to keep in mind is the strandedness of the evidence and the model (they must be on the same strand). Further protein evidence is only valid support if it is in the same reading frame as the model.</div><div><br></div><div>Could you send the full GFF3 for the contig (I need features and GFF3 internal fasta) and the coordinates of the region in question, and I can take a look? Also if you can, it would be good to let maker run Augustus as well with the species file rather than just passing in the GFF3. This is because MAKER can only talk to Augustus to generate competing hint based models if you provide the species.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Innocent Onsongo <<a href="mailto:onson001@umn.edu">onson001@umn.edu</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 5 June, 2013 1:10 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Carson Holt <<a href="mailto:carson.holt@oicr.on.ca">carson.holt@oicr.on.ca</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>, Barry Moore <<a href="mailto:barry.utah@gmail.com">barry.utah@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Maker: accessory scripts<br></div><div><br></div><div dir="ltr">I checked visually in IGV and there are some exons in the predicted model with protein and EST support but the maker output GFF only has match_part and protein_match in column 3. Does that mean Maker doesn't deem any of the evidence sufficient to make a gene model prediction? <div><br></div><div style="">I guess I am somewhat surprised I am not getting any exons predicted by Maker. Is there a parameter I can alter to reduce the threshold at which Maker makes this call? I have attached the first 400 lines of one of my GFF files together with the control file (maker_opts.ctl) just in case they might be useful. </div><div style=""><br></div><div style="">Getiria </div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jun 5, 2013 at 9:47 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>Also, just a note, models are rejected if they have no protein or EST support. This is because ab inito predictors over predict (you may have 10 false positives for every true positive in some genomes for example).</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 5 June, 2013 10:44 AM<br><span style="font-weight:bold">To: </span> Innocent Onsongo <<a href="mailto:onson001@umn.edu" target="_blank">onson001@umn.edu</a>>, Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>><div class="im"><br><span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>>, Barry Moore <<a href="mailto:barry.utah@gmail.com" target="_blank">barry.utah@gmail.com</a>><br></div><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Maker: accessory scripts<br></div><div><div class="h5"><div><br></div><div><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>All maker gene annotations will be of the format gene/mRNA/exon/CDS. Anything in the format match/match_part is an evidence alignment or rejected model and is there for reference purposes. If you want to upgrade all of the rejected loci to gene annotations, set keep_preds=1 in the control files. If you want to upgrade a subset of rejected models to a full annotation, create a list of IDs (one per line) then give them to the attached script. gff3_preds2models was previously deprecated and no longer part of the maker distribution, but the attached script is an updated version with the same functionality. </div><div><br></div><div>--Carson</div><div><br></div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Innocent Onsongo <<a href="mailto:onson001@umn.edu" target="_blank">onson001@umn.edu</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 5 June, 2013 12:35 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>><br><span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>>, Barry Moore <<a href="mailto:barry.utah@gmail.com" target="_blank">barry.utah@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Maker: accessory scripts<br></div><div><br></div><div dir="ltr">I was able to successfully ran Maker and now want to c<span style="line-height:19px;font-size:13px;font-family:sans-serif">onverts the gene prediction match/match_part format to annotation gene/mRNA/exon/CDS format. I looked at the tutorial and the script </span><span style="line-height: 19px; font-size: 13px; background-color: rgb(249, 249, 249); font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">gff3_preds2models</span><div><span style="line-height:19px;font-size:13px;font-family:sans-serif">is supposed to do this conversion. How do I access this script. It is not in </span>/maker/2.28-beta/bin/<br></div><div><br></div><div>Also, in running <span style="line-height: 19px; font-size: 13px; background-color: rgb(249, 249, 249); font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">gff3_preds2models <gff3 file> <pred list> </span> is <<span style="line-height: 19px; font-size: 13px; background-color: rgb(249, 249, 249); font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">pred list> the file I used for </span><span style="line-height: 19px; font-size: 13px; background-color: rgb(249, 249, 249); font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">pred_gff=? </span></div><div><span style="line-height: 19px; font-size: 13px; background-color: rgb(249, 249, 249); font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; "><br></span></div><div>Long story short, how do I transform the GFF output from Maker to the more traditional annotation of exon/intron? <br></div><div><br></div><div><span style="line-height: 19px; font-size: 13px; background-color: rgb(249, 249, 249); font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">Thanks, </span></div><div>Getiria</div></div>
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University of Minnesota<br>Minneapolis, MN 55455<br>Phone: 612-624-0532
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