<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); "><div style="font-family: Calibri, sans-serif; font-size: 14px; ">You need to convert the GTF files to GFF3. There is a tophat2gff and cufflinks2gff script that come with MAKER. I recommend only using cufflinks results and ignoring tophat results though as they tend to be a lot more spurious.</div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><div style="font-family: Calibri, sans-serif; font-size: 14px; ">Jason Stajich wrote an excellent explanation on training Augustus on the <span class="Apple-style-span" style="font-family: Calibri; font-size: medium; ">list previously - </span><span class="Apple-style-span" style="font-family: Calibri; font-size: medium; "><a href="http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html">http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html</a></span></div><div><div><div style="font-family: Calibri; font-size: medium; ">He also included scripts to assist with the training - <a href="https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl">https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl</a></div></div></div><div style="font-family: Calibri; font-size: medium; "><br></div><div style="font-family: Calibri; font-size: medium; ">Overall the strategy is similar to the one used to train SNAP.</div><div style="font-family: Calibri; font-size: medium; "><br></div><div style="font-family: Calibri; font-size: medium; ">Thanks,</div><div style="font-family: Calibri; font-size: medium; ">Carson</div><div style="font-family: Calibri; font-size: medium; "><u><br></u></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><span id="OLK_SRC_BODY_SECTION" style="font-size: 14px; font-family: Calibri, sans-serif; "><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> 熹熹 <<a href="mailto:linzkl007@hotmail.com">linzkl007@hotmail.com</a>><br><span style="font-weight:bold">Date: </span> Saturday, 11 May, 2013 1:28 PM<br><span style="font-weight:bold">To: </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>><br><span style="font-weight:bold">Subject: </span> [maker-devel] about predictor training<br></div><div><br></div><div><style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 12pt;
font-family:微?雅?
}
--></style><div class="hmmessage"><div dir="ltr">Hi,<br><br>I'm trying to use MAKER to annotate the new genome sequence which I assembled by myseft. I used TopHat and Cufflinks to align the sequence based on the RNA-seq we have. Based on the tutorial of MAKER, I may need three fasta format file including assembly data, ESTs and protein database to train the SNAP. I may use SwissProt as the protein database. Can I use the gtf result from Cufflinks directly as an ESTs during the training? <br>Another is, if I want to use Augustus to do the ab initio gene prediction, do I need to do the same way as SNAP? Cause I saw some posts that the result from ab initio would be used as the evidence to train the predictor. Can I ask is there has some order doing the prediction in different predictor?<br><br>Thank you so much for you help.<br><br>Lin<br> </div></div></div>_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></body></html>