[maker-devel] Generating GFF with selected tracks

[Felipe Barreto]

OK, I see.  I will just use grep to extract the desired features from the
full.gff and merge them with gff3_merge.  Don't know why I was making it
more complicated.  I guess I don't understand gff formats very well quite
yet.

Thanks yet again!


On Thu, Jun 5, 2014 at 12:08 PM, Daniel Ence <dence at genetics.utah.edu>
wrote:

>  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
> 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>
>  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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>
>
>


-- 
Felipe Barreto
Post-doctoral Scholar
Scripps Institution of Oceanography
University of California, San Diego
La Jolla, CA 92093
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