<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Also Xiaofang, you mentioned that you have used SOBA, there is a command line version (called SOBAcl) that hasn't been advertised too well that does a lot more than the web version in terms of comparison and reporting. You can find it here:</div><div><br></div><div><a href="http://www.sequenceontology.org/resources/sobacl.html">http://www.sequenceontology.org/resources/sobacl.html</a></div><div><br></div><div>It can prepare tables and graphs on multiple GFF3 for feature counts, lengths, footprints etc.</div><div><br></div><div>Mike Campbell here in the lab has a script to generate the data necessary for AED figures like this one and he's going to add it to maker/bin some time in the near future.</div><div><br></div><div><img alt="An external file that holds a picture, illustration, etc.
Object name is 1471-2105-12-491-3.jpg" title="Click on image to zoom" class="tileshop" src="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280279/bin/1471-2105-12-491-3.jpg"></div><div><br></div><div>B</div><div><br></div><div><div>On Aug 23, 2013, at 11:41 AM, Daniel Ence wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Xiaofang, <br><br>1. People use various ad-hoc scripts for comparing genome genome annotations. If you look in the MAKER2 paper(Holt and Yandell, BMC Bioinformatics 2011), you'll see the AED score, which is some we use to compare the support from the evidence. <br><br>2.<br>It actually isn't surprising that you got that big of an increase in the number of genes when you turned "keep_preds" to 1. Ab-initio predictors give a great many false positives and "keep_preds=1" will turn all of those into gene models. <br><br>To get more genes, you should probably train an additional gene predictor, like GeneMark and maybe augustus. I think that augustus should already have a config file for mosquito. <br><br>Changing the "pred_flanks" will increase the number of genes if you think that you have many merged genes. <br><br>What protein dataset did you use? We often use a set from a comprehensive protein database like uniprot in addition to proteins from closely related species. <br><br>Thanks,<br>Daniel<br>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<br>________________________________________<br>From: maker-devel [<a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a>] on behalf of Xiaofang Jiang [<a href="mailto:jxf1023@gmail.com">jxf1023@gmail.com</a>]<br>Sent: Thursday, August 08, 2013 7:11 PM<br>To: <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br>Subject: [maker-devel] annotation comparison<br><br>Dear Maker Developers,<br><br>I am annotating a mosquitoes genome using Maker. I have two questions<br>regarding Maker annotation.<br><br>1. Are there any scripts available to compare two sets of annotations?<br>We know about SOBA but were wondering if there is something more<br>comprehensive that you guys use.<br><br>2. I am expecting around 13,000 genes, however maker only predicted<br>9,000 genes. I used both the gff3 from cufflinks, protein, and ESTs as<br>evidence and SNAP as the ab inito predictor. I changed "keep_preds" to 1<br>and that resulted 17,000 genes, it seems that shouldn't have happened.<br>So in order to get more genes, should I try change "single_length" to<br>100, and change "pred_flanks" to 100?<br><br><br>Best,<br><br>Xiaofang<br><br><br>_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br><br>_______________________________________________<br>maker-devel mailing list<br>maker-devel@box290.bluehost.com<br>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br></div></blockquote></div><br><div apple-content-edited="true">
<div><div style="font-family: Arial; font-size: 12px; ">Barry Moore</div><div style="font-family: Arial; font-size: 12px; ">Research Scientist</div><div style="font-family: Arial; font-size: 12px; ">Dept. of Human Genetics</div><div style="font-family: Arial; font-size: 12px; ">University of Utah</div><div style="font-family: Arial; font-size: 12px; ">Salt Lake City, UT 84112</div><div style="font-family: Arial; font-size: 12px; ">--------------------------------------------</div><div style="font-family: Arial; font-size: 12px; ">(801) 585-3543</div><div style="font-family: Arial; font-size: 12px; "><br class="khtml-block-placeholder"></div></div><div><br></div><br class="Apple-interchange-newline">
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