[maker-devel] Generating GFF with selected tracks

[Carson Holt]

gff3_merge just merges any two GFF3 files.  So if you have two files just
give both of them to it.

Example -->
gff3_merge maker_genes.gff repeats.gff

Also if all you are trying to do is filter out certain feature types from
the file, just use grep instead.

Example -->
grep -v -P "\tpred_gff\t" maker.gff

Thanks,
Carson


From:  Felipe Barreto <fbarreto at ucsd.edu>
Date:  Thursday, June 5, 2014 at 1:01 PM
To:  MAKER group <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Generating GFF with selected tracks

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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