<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">If you are running with different settings on the exact same contig, you will have to merge the models using the -l legacy option of gff3_merge to ensure there will be no ID collisions (some things will have the same IDs in the different runs).<div class=""><br class=""></div><div class="">Then supply just the genes to pred_gff on the rerun.</div><div class=""><br class=""></div><div class="">Alternatively you could have just provided your different predictor files as a comma separated list (i.e. snaphmm=hmm1,hmm2,hmm3). MAKER would have ran each one and kept just the one that best matched the evidence.</div><div class=""><br class=""></div><div class="">However because MAKER passes hints to the predictors (which override the HMM for the most part), I have found that running with different predictor settings because of GC differences between contigs doesn’t provide the benefit you would think.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 1, 2016, at 12:17 PM, Arun Seetharam <<a href="mailto:arnstrm@gmail.com" class="">arnstrm@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi Daniel,<br class=""><br class=""></div>Thanks very much for the reply! It is the latter: same input genome under 3 settings (training was done using a different set of genes for all the gene predictors). I simply want to get a single gff, retaining only the best model(s) for each locus.<br class="">Are you suggesting that I can run MAKER by providing 3 files for "maker_gff" (in maker_opts.ctl) and keeping everything else default? or do I have to do something in the CTL file to achieve this? I appreciate if you can provide more details for how to do this!<br class=""><br class="">Thanks once again for the reply!<br class=""><div class="gmail_extra"><br class=""><div class="gmail_quote">On Fri, Jan 1, 2016 at 12:37 PM, Daniel Ence <span dir="ltr" class=""><<a href="mailto:dence@genetics.utah.edu" target="_blank" class="">dence@genetics.utah.edu</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Arun, are the three rounds of maker on different parts/versions of the genome or did you maker on the same genome with three different settings? If it’s the former, then you can merge the maker gff files with gff3_merge, which is included with your maker installation.<br class="">
<br class="">
If it’s the latter case then I do think EVM could help if you want to give the different result sets different confidence weights. If you want to give them all the same weight, then you could do another run of maker, and pass them through as either models or predictions.<br class="">
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~Daniel<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
Daniel Ence<br class="">
Graduate Student<br class="">
Eccles Institute of Human Genetics<br class="">
University of Utah<br class="">
15 North 2030 East, Room 2100<br class="">
Salt Lake City, UT 84112-5330<br class="">
<div class=""><div class="h5"><br class="">
> On Jan 1, 2016, at 11:31 AM, Arun Seetharam <<a href="mailto:arnstrm@gmail.com" class="">arnstrm@gmail.com</a>> wrote:<br class="">
><br class="">
> Hi all,<br class="">
><br class="">
> First of all, a very happy new year to all of you! I hope everyone is having a great holiday season.<br class="">
><br class="">
> I have a question about Maker. For my grass species, I ran 3 separate rounds of MAKER (low GC, regular GC and high GC) and I now have 3 maker gff files. So, what is the correct way to merge these files to a single gff file? Do I have to run a maker round with just the GFF files as input? It looks like EVM especially meant to do this kind of job, but not sure if Maker does this too.<br class="">
><br class="">
> Thanks for any help or suggestions!<br class="">
><br class="">
> Have a nice day,<br class="">
> --<br class="">
> Arun Seetharam<br class="">
> Post Doctoral Research Associate<br class="">
> Genome Informatics Facility & EEOB<br class="">
> Office of Biotechnology<br class="">
> 228 Science I<br class="">
> Iowa State University<br class="">
> Ames, Iowa 50011<br class="">
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</blockquote></div><br class=""><br clear="all" class=""><br class="">-- <br class=""><div class="gmail_signature"><div dir="ltr" class="">Arun Seetharam<br class="">Post Doctoral Research Associate<br class="">Genome Informatics Facility & EEOB<br class="">Office of Biotechnology<br class="">228 Science I<br class="">Iowa State University<br class="">Ames, Iowa 50011</div></div>
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