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<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">Dear Maker developers,</span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">1. We use assembled RNAseq(from same species) and protein evidence(from evolutionary close species) to generate training gene structure(1st iteration, est2genome=1,protein2genome=1
). <br>
</span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">2. This is than used to train abinito gene predictors, SNAP and AUGUSTUS. <br>
</span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">3. GeneMarkES( version: GeneMark-ES / ET v.4.32) is used to produce training data-set with the command</span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">gmes_petap.pl --sequence pmin_jelly.fa<br>
</span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">4. We would be predicting genes using results from SNAP, Genemark and AUGUSTUS(2nd iteration, est2genome=0, protein2genome=0) </span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">I have couple of questions relating to Genemark and AUGUSTUS</span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">1. AUGUSTUS</span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">We do not have a species file for species file of our interest or evolutionary closer species</span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">following command is used to generate species file</span></font></p>
<p></p>
<div><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">/autoAug.pl --genome=pmin_jelly.fa --species=pminiata --cdna=pmin_transcripts.fa --trainingset=genome.gff3 --singleCPU -v --useexisting <br>
</span></font></div>
<b style="background-color: rgba(255, 255, 255, 0);"><font color="#000000">AUGUSTUS is taking too long to compute species file, is there a solution for this issue. Using species file from other organism might generate false positives. Is it advised in such
situations to not used AUGUSTUS model?</font></b>
<p></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);"><b></b>2. Genemark<br>
</span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">I used the gmhmm file generated in the genemark output directory, however I encounter following error</span></font></p>
<p></p>
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<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">-------------------------<br>
</span></font></p>
<div><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);"><b>STATUS: Parsing control files...<br>
ERROR: You have failed to provide a value for 'gmhmme3' in the control files.<br>
ERROR: You have failed to provide a value for 'probuild' in the control files.</b><br>
</span></font></div>
<font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">---------------------</span></font></div>
<font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">FYI</span></font>
<p></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">-----<br>
</span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">maker_opts.ctl<br>
</span></font></p>
<p></p>
<div><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">#-----Gene Prediction<br>
snaphmm=/home/parul/Pmin_new/maker_snap/pmin1.hmm #SNAP HMM file<br>
gmhmm=/home/parul/Pmin_new/maker_snap/gmhmm.mod #GeneMark HMM file<br>
</span></font></div>
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<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">-----<br>
</span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">Using SNAP for training gene model yields over 6000-7000 additional gene. The model has good cumulative AED value. <br>
</span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">I was hoping in addition to SNAP, if I could use AUGUSTUS and GeneMark to train the gene model to fuse dispersed models so that the gene count is within the expected range.</span></font></p>
<p><br>
</p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">Thanks and regards,</span></font></p>
<p><font color="#000000"><span style="background-color: rgba(255, 255, 255, 0);">Parul<br>
</span></font></p>
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<span>Sent from my iPhone</span><br>
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