<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>Alternatively you can play with the individual filtering thresholds in maker2zff. Given you have > 13000 models to train with, you probably want to par that down to a couple of thousand.</div><div><br></div><div>—Carson</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> mun hua <<a href="mailto:mh.tan85@gmail.com">mh.tan85@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, December 2, 2013 at 6:28 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</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>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] empty maker2zff output<br></div><div><br></div><div dir="ltr">Hi Carson,<div><br></div><div>Thanks for the reply.</div><div>I used maker2zff -n which successfully generated zff and dna files. Since no filters were applied, this means that no filtering of AED values were done on the dataset. Would this give too many incorrect hints for training?</div><div><br></div><div>Also, after running maker2zff, I ran a fathom -gene-stats on the output files:</div><div><br></div><div><div>8715 sequences</div><div>0.438058 avg GC fraction (min=0.347801 max=0.759494)</div><div>15186 genes (plus=7550 minus=7636)</div><div>1497 (0.098578) single-exon</div><div>13689 (0.901422) multi-exon</div><div>171.161285 mean exon (min=1 max=17109)</div><div>792.466980 mean intron (min=1 max=23667)</div></div><div><br></div><div>When I do a fathom -validate, it lists down a lot of errors, mostly on misordered genes and overlapping exons. Is this expected? The organism I am annotating is fish.</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Dec 3, 2013 at 7:15 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>Set protein2genome=1. Even then you may noir get many results, but on a whole genome you should get a few hundred that match uniprot enough to make an annotation directly from protein.</div><div><br></div><div>Then with maker2zff use the -n flag to turn off all filtering, otherwise you won’t get any results (too little evidence support).</div><div><br></div><div>For the example not working, it is because it has really long UTRs, and one of the default filters was set slightly too high for the example in 2.28 for it to give est2genome results, but SNAP should still produce results. The filter was brought back down in 2.29 and 2.30.</div><div><br></div><div>—Carson</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> mun hua <<a href="mailto:mh.tan85@gmail.com" target="_blank">mh.tan85@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, December 2, 2013 at 12:18 AM<br><span style="font-weight:bold">To: </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>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] empty maker2zff output<br></div><div><div class="h5"><div><br></div><div dir="ltr">Hi,<div><br></div><div>I noticed that this empty output may be because I am only using SwissProt protein sequences as evidence, because I do not have any EST or transcript data generated for my organism.</div><div><br></div><div>My question is, how does one proceed to train and generate final annotation starting with only the assembled genome sequence and UniProt/SwissProt sequences?</div><div><br></div><div>Please advise.</div><div><br></div><div>Thanks very much.</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Dec 2, 2013 at 11:53 AM, mun hua <span dir="ltr"><<a href="mailto:mh.tan85@gmail.com" target="_blank">mh.tan85@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 dir="ltr">Hi<div><br></div><div>I'm trying to create training data for SNAP using the maker2zff script that comes with the maker package version 2.28.</div><div>I'm having the same problem as mentioned in this post: <a href="https://groups.google.com/forum/#!searchin/maker-devel/maker2zff/maker-devel/_Pq65Fb761U/s826h5lSxnYJ" target="_blank">https://groups.google.com/forum/#!searchin/maker-devel/maker2zff/maker-devel/_Pq65Fb761U/s826h5lSxnYJ</a></div><div>My genome.ann and genome.dna files are empty, but no errors were printed.</div><div><br></div><div>Any advice on this?</div><div><br></div><div>Thanks.</div><span><font color="#888888"><div>Mun Hua</div></font></span></div></blockquote></div><br></div></div></div></div>
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