<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>Could you pick one contig where the number of genes shift dramatically and upload that contig fasta together with your control files and any evidence datasets used to one of our servers (I'm going to send you connection details in a separate e-mail). I can then run with and without correct_est_fusion to see if there is anything unexpected going on.</div><div><div><br></div><div><p style="line-height: 19px; font-size: 13px; margin: 0.4em 0px 0.5em; font-family: sans-serif; ">--Carson</p></div></div><div><br></div><div><br></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> Benjamin Rubin <<a href="mailto:brubin@fieldmuseum.org">brubin@fieldmuseum.org</a>><br><span style="font-weight:bold">Date: </span> Tuesday, August 27, 2013 10:59 AM<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>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Unexpected results with correct_est_fusion<br></div><div><br></div><div dir="ltr">Hi Carson,<div><br></div><div>I increased pred_flank to 200 and reran MAKER with correct_est_fusion, but I still only get ~5,000 genes (5,082 instead of the 5,020 with pred_flank at 100). This is using only the first round with SNAP and Augustus trained on the CEGMA genes. Is there anything else that I might be doing wrong? I have attached my control file in case that could be useful.<br></div><div><br></div><div>Thanks for the help!</div><div>Ben</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Aug 26, 2013 at 2:00 PM, 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>The correct_est_fusion option just clips UTR on overlapping genes. I suspect the real problem is setting pred_flank too low. If your lead in sequence to a gene is too short, ab initio predictors won't call it. So you are probably getting empty reports from SNAP/Augustus for the hint based predictions. Try increasing pred_flank to at least 150. Setting pred_flank too low will also limit how far MAKER will walk out along the edges initial alignments during the polishing step (exonerate). So setting it too low may also be causing you to lose some EST and protein alignments.</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> Benjamin Rubin <<a href="mailto:brubin@fieldmuseum.org" target="_blank">brubin@fieldmuseum.org</a>><br><span style="font-weight:bold">Date: </span> Monday, August 26, 2013 2:20 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Unexpected results with correct_est_fusion<br></div><div><div class="h5"><div><br></div><div dir="ltr"><div>Hello developers,</div><div><br></div>I am using MAKER 2.28 to annotate an ant genome. I provide protein sequence evidence from all seven of the other sequenced ant genomes and a <i>de novo</i> assembled transcriptome as EST evidence. I assembled the transcriptome using Trinity with the jaccard_clip option turned on to reduce gene fusions. Despite using this set of hopefully non-fused ESTs, I still have substantial fusion problems with the final annotation. Therefore, I reduced pred_flank to 100 and turned on correct_est_fusion. However, correct_est_fusion leads to the prediction of a much smaller number of genes (~5,000 instead of ~14,000). I am initially training both SNAP and Augustus using CEGMA genes and then retraining based on the first round of annotation. Both rounds of annotation yield the same low number (~5,000) of genes. It may also be worth mentioning that the number of exons is also far lower when using correct_est_fusion (~26,000 instead of ~90,000).<div><br></div><div>Is this the expected behavior of correct_est_fusion? I was surprised that it reduced the predicted number of genes by such a large margin. I am concerned that I am using it incorrectly. Do you have any other suggestions for reducing gene merging?</div><div><br></div><div>Thanks,</div><div>Ben<br clear="all"><div><br></div>-- <br><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">_____________________________________________________<br>Benjamin ER Rubin</span><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">PhD Candidate</span><div><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><span style="border-collapse:separate;font-family:arial;font-size:small"><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">Committee on Evolutionary Biology</span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">University of Chicago</span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><a href="http://www.moreaulab.org/Benjamin_Rubin.html" style="color:rgb(6,88,181)" target="_blank">http://www.moreaulab.org/Benjamin_Rubin.html</a></span></div></span></span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br></span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">Division of Insects<br>
Zoology Department<br>Field Museum of Natural History<br>1400 South Lake Shore Drive<br>Chicago, IL 60605<br>USA<br>Office: <a href="tel:%28312%29%20665-7776" value="+13126657776" target="_blank">(312) 665-7776</a></span></div></div></div></div></div></div>
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Zoology Department<br>Field Museum of Natural History<br>1400 South Lake Shore Drive<br>Chicago, IL 60605<br>USA<br>Office: (312) 665-7776</span></div></div></div></span></body></html>