<div dir="ltr">Thanks for the timely feedback Carson. I made a change to my pred_gff and est_gff GFF3 files and now I am getting results but I am not sure if the changes I made are valid. I want to make sure the changes I made did not lead Maker to behave in an unexpected way and lead to results that might be incorrect. <div>
<br></div><div>In my pred_gff file, I replaced "mRNA" with "protein_match" and "exon" with "match" below are the first three lines of the old and new pred_gff files respectively<div style>
<br></div><div style>---------------old pred_gff</div><div style><div>##gff-version 3</div><div>CGS00003 AUGUSTUS mRNA 1 10865 1 + . </div><div>CGS00003 AUGUSTUS exon 2013 2050 . + 1 </div>
<div><br></div><div>---------------new pred_gff<br></div><div>##gff-version 3<br></div><div><div>CGS00003 AUGUSTUS protein_match 1 10865 1 + . </div><div>CGS00003 AUGUSTUS match_part 2013 2050 . + 1 </div>
</div><div><br></div><div>In my est_gff file, I replaced "mRNA" with "protein_match" and "exon" with "match" below are the first three lines of the old and new pred_gff files respectively<br>
</div><div><br></div><div style>----------------old est_gff</div><div><div>##gff-version 3</div><div>CGS00003 EST_BLAT mRNA 4641336 4758501 6072 - . </div><div>CGS00003 EST_BLAT exon 4641336 4641979 644 - . </div>
</div><div><br></div><div>----------------new est_gff<br></div><div><div>CGS00003<span class="" style="white-space:pre"> </span>EST_BLAT<span class="" style="white-space:pre"> </span>expressed_sequence_match<span class="" style="white-space:pre"> </span>4641336<span class="" style="white-space:pre"> </span>4758501<span class="" style="white-space:pre"> </span>6072<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span></div>
<div>CGS00003<span class="" style="white-space:pre"> </span>EST_BLAT<span class="" style="white-space:pre"> </span>match_part<span class="" style="white-space:pre"> </span>4641336<span class="" style="white-space:pre"> </span>4641979<span class="" style="white-space:pre"> </span>644<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span></div>
</div><div><br></div><div style>Are the changes I made valid?</div><div style><br></div><div style>Thanks, </div><div style>Getiria</div><div><br></div><div><br></div></div></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>
_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></span></div>
</div></div></div></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Getiria Onsongo, Ph.D.<br>Informatics Analyst, Research Informatics Support System<br>Minnesota Supercomputing Institute for Advanced Computational Research<br>
University of Minnesota<br>Minneapolis, MN 55455<br>Phone: 612-624-0532
</div>