<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">It seems to have disappeared completely. I'm running MAKER again now using the tophat alignments that I fed to cufflinks, instead of the cufflinks data. So far the two models visually checked as missing with the cufflinks data are present as they should be. I have to wait for the run to finish to get a whole genome count though. Maybe I need to look more closely at the cufflinks run that I did. <div><br></div><div>The RNA-Seq data are from the NCBI SRA and I didn't do anything to clean them up before I ran tophat.<br><div><br></div><div><br><div><div>On Oct 2, 2012, at 9:10 AM, Daniel Hughes <<a href="mailto:dsthughes@gmail.com">dsthughes@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><p>Did the whole model vanish or just the protein product - contaminated rnaseq that hasn't been cleaned up enough will regularly cause the later to become part of a bad utr.</p><p>Dan</p>
<div class="gmail_quote">On Oct 2, 2012 6:01 AM, "Michael Thon" <<a href="mailto:mike.thon@gmail.com">mike.thon@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">I looked at two cases in which the model_gff disappeared and they occurred in regions where there are multiple overlapping cufflinks features. One model that I'm looking at right now has overlapping protein2genome and a SNAP feature overlapping it but it was still not included in the output. it could be a problem in MAKER or it could be a problem with my RNA Seq data. I aligned the RNA Seq data using tophat/cufflinks and converted the transcripts.gtf file to gff using cufflinks2gff3 script.<div>
<br></div><div>Is it better to use RNA Seq feature from tophat or cufflinks?</div><div><br><div><br><div><div>On Oct 1, 2012, at 4:01 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:</div>
<br><blockquote type="cite"><div style="word-wrap:break-word;font-size:14px;font-family:Calibri,sans-serif"><div>They can be replaced under two circumstances. </div><div>1. If you provide two model_gff files (comma separated list), in which case MAKER thinks it is merging legacy annotations and will only keep one or the other if models overlap. </div>
<div>2. If you turn snap, augusutus, genemark, or est2genome on. MAKER sees this as a cue that if these other programs produce a better model, it can replace the current model. If you set map_forward=1, MAKER will conserve the name of the previous model (so models change structure but names are conserved); otherwise, it gets a new name. Sometimes groups like to rename models every time their is a structural change. I think you are supposed to get the Alias attribute set when you don't get names mapped forward though (I can't remember if I added this or just planned on adding the Alias mapping though).</div>
<div><br></div><div>MAKER should never drop a model_gff model. It can only replace it if something better comes along, but it should not disappear.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div>
<br></div><span><div style="font-family:Calibri;font-size:11pt;text-align:left;border-width:1pt medium medium;border-style:solid none none;padding:3pt 0in 0in;border-top-color:rgb(181,196,223)"><span style="font-weight:bold">From: </span> Michael Thon <<a href="mailto:mike.thon@gmail.com" target="_blank">mike.thon@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span> Monday, 1 October, 2012 1:53 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>><br>
<span style="font-weight:bold">Subject: </span> [maker-devel] model_gff question<br></div><div><br></div><div><div style="word-wrap:break-word">Under what circumstances will maker not include a gene model from the model_gff file in its final output? It was my understanding from this post:<div>
<a href="https://groups.google.com/d/topic/maker-devel/Y5jSdZ1Olcc/discussion" target="_blank">https://groups.google.com/d/topic/maker-devel/Y5jSdZ1Olcc/discussion</a></div><div><br></div><div>That maker will keep or replace models in model_gff and never remove them. I'm reannotating a fungal genome and in model_gff I'm providing the gene models originally made by the sequencing center. I have 12006 models in the file I specify in model_gff but maker's final annotation has only 10727 models in it. </div>
<div>-Mike</div><div><br></div></div></div>_______________________________________________
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