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Hi Felipe, I seem to remember that some of the gene model names did change when I did things similar to what you described. I think that you could accomplish the same thing with some cat and grep commands on the full gff. That would avoid the trouble of rerunning
maker. Something like "cat full.gff | grep -P "\trepeatrunner\t" > tmp.gff " would get you started.
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<div>~Daniel</div>
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<div><span style="font-family: Tahoma; font-size: small; ">Daniel Ence</span></div>
<div><span style="font-family: Tahoma; font-size: small; ">Graduate Student</span></div>
<div><a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">Eccles Institute of Human Genetics</span><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">University of Utah</span><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">15 North 2030 East, Room 2100</span><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">Salt Lake City, UT 84112-5330</span></div>
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<div>On Jun 5, 2014, at 12:01 PM, Felipe Barreto <<a href="mailto:fbarreto@ucsd.edu">fbarreto@ucsd.edu</a>></div>
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<div dir="ltr">Hi, all,
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<div>I would like to produce a gff file that contains Maker gene models AND repeats. I know that using gff3_merge with -g will generate one with only the gene models, but I didn't see any options for adding additional tracks.</div>
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<div>The way I did this was to use the Re-annotation section in the control file. I provided the original full gff file in maker_gff, and turned on the rm_pass and model_pass. All other options in the control file were turned off. This seemed to work, though
it also added a 'model_gff:maker' track, which is not a problem for me. I compared a few new and original scaffolds in Apollo, and all seem to match perfectly. But since I cannot check the whole genome, I was wondering if what I did was appropriate. Are
all the gene models (and their names) and repeat alignments identical between the new and original files? Or is Maker potentially changing a few things since it's treated as a new run?</div>
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<div>Thanks!<br clear="all">
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-- <br>
Felipe Barreto<br>
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