<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>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 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> Carson Holt <<a href="mailto:carsonhh@gmail.com">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">onson001@umn.edu</a>>, Carson Holt <<a href="mailto:carson.holt@oicr.on.ca">carson.holt@oicr.on.ca</a>><br><span style="font-weight:bold">Cc: </span> "<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><div 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>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 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 12:35 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carson.holt@oicr.on.ca">carson.holt@oicr.on.ca</a>><br><span style="font-weight:bold">Cc: </span> "<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> [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="color:rgb(0,0,0);font-family:sans-serif;font-size:13px;line-height:19px">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="background-color: rgb(249, 249, 249); color: rgb(0, 0, 0); font-size: 13px; line-height: 19px; font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">gff3_preds2models</span><div style=""><span style="color:rgb(0,0,0);font-family:sans-serif;font-size:13px;line-height:19px">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 style=""><br></div><div style="">Also, in running <span style="background-color: rgb(249, 249, 249); color: rgb(0, 0, 0); font-size: 13px; line-height: 19px; font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">gff3_preds2models <gff3 file> <pred list> </span> is <<span style="background-color: rgb(249, 249, 249); color: rgb(0, 0, 0); font-size: 13px; line-height: 19px; font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">pred list> the file I used for </span><span style="background-color: rgb(249, 249, 249); color: rgb(0, 0, 0); font-size: 13px; line-height: 19px; font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">pred_gff=? </span></div><div style=""><span style="background-color: rgb(249, 249, 249); color: rgb(0, 0, 0); font-size: 13px; line-height: 19px; font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; "><br></span></div><div style="">Long story short, how do I transform the GFF output from Maker to the more traditional annotation of exon/intron? <br></div><div style=""><br></div><div style=""><span style="background-color: rgb(249, 249, 249); color: rgb(0, 0, 0); font-size: 13px; line-height: 19px; font-family: 'Lucida Console', Monaco, 'Courier New', Courier, monospace; ">Thanks, </span></div><div style="">Getiria</div></div>
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