[maker-devel] Generating GFF with selected tracks

[Daniel Ence]

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.

~Daniel


Daniel Ence
Graduate Student
dence at genetics.utah.edu<mailto:dence at genetics.utah.edu>
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

On Jun 5, 2014, at 12:01 PM, Felipe Barreto <fbarreto at ucsd.edu<mailto:fbarreto at ucsd.edu>>
 wrote:

Hi, all,

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.

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?

Thanks!

--
Felipe Barreto

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