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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Felipe,
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<div>I think 1500 models sounds like a good size set with which to train SNAP. I think that SNAP expects ~1000 models for training. </div>
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<div>The only other comment on the approach is perhaps that using only one ab-initio predictor is a little bit risky. Using multiple predictors would allow MAKER to select from among their different models for the one that best fits the evidence. </div>
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<div>Good luck and let us know if there's anything we can help with!</div>
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Thanks,</div>
<div>Daniel<br>
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<div class="PlainText">Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330</div>
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<div id="divRpF54511" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> maker-devel [maker-devel-bounces@yandell-lab.org] on behalf of Felipe Barreto [fbarreto@ucsd.edu]<br>
<b>Sent:</b> Tuesday, March 18, 2014 10:08 AM<br>
<b>To:</b> MAKER group<br>
<b>Subject:</b> [maker-devel] Size of initial EST training set for SNAP<br>
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<div dir="ltr"><span style="font-family:arial,sans-serif; font-size:12.727272033691406px">Hi, all,</span>
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<div style="font-family:arial,sans-serif; font-size:12.727272033691406px">I've been learning a lot from reading posts from this group, and finally started doing actual runs of Maker on our current genome assembly (arthropod, genome size ~230Mb). I started
by training SNAP, but would like to check my approach before continuing with longer runs. </div>
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<div style="font-family:arial,sans-serif; font-size:12.727272033691406px">From our full set of ~40,000 ESTs (RNA-seq assembly), I chose ~2000 that I deemed of very high quality based on blast alignments to Swiss-Prot (based on query-subject coverage, bit score,
etc). I then used only these 2000 ESTs in a first Maker run using est2genome=1. The output returned 1500 models (with the 500 "missing" models probably a result of single-exon issues; not a concern at this point).</div>
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<div style="font-family:arial,sans-serif; font-size:12.727272033691406px">I now plan on training SNAP with this first output, and then doing another Maker run now using: 1) all ESTs (but est2genome=0), 2) my chosen protein evidence, and 3) SNAP with the first
HMM file. The output of this second run will be used to re-train SNAP, and this second HMM file will be used in a final "official" run (while continuing to provide the EST and protein evidence, of course).</div>
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<div style="font-family:arial,sans-serif; font-size:12.727272033691406px">Does this sound like a reasonable approach? Simply put, my main concern is whether I'm using too few ESTs in my first est2genome step.</div>
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<div style="font-family:arial,sans-serif; font-size:12.727272033691406px">Thanks for any insight!</div>
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-- <br>
Felipe Barreto<br>
Post-doctoral Scholar<br>
Scripps Institution of Oceanography<br>
University of California, San Diego<br>
La Jolla, CA 92093 </div>
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