[maker-devel] Generating GFF with selected tracks

[Felipe Barreto]

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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