[maker-devel] Other GFF not passed through

[Carson Holt]

gff3_merge is expecting to work with maker output, and the -g option specifically looks for maker produced genes (maker source tag).  Since you added these lines using the other_gff option, they are in the file, but it doesn’t necessarily mean downstream maker tools will know what to do with them because maker added them blindly without attempting any interpretation/validation, etc.  I purposely don’t try and make these tools support any GFF3 input possible, it just gets too hairy.

What you can do though is grep the features you want out separately into another GFF3 file and then you can use gff3_merge to combine those two files.

grep -P “\tbarrnap:0.5\t” infile.gff > barnap.gff
gff3_merge -s maker.gff barnap.gff > new.gff

Thanks,
Carson


> On May 1, 2015, at 1:34 PM, Shaun Jackman <sjackman at gmail.com> wrote:
> 
> Hi, Carson.
> 
> I’m using other_gff to pass the following four-record GFF file of rRNA annotations through to the final GFF file. The rRNA records appear in the output of gff3_merge -s -n, but not when I add the -g option. Any thoughts why they’ve gone missing? These rRNA features almost certainly overlap repeat rRNA features discovered by RepeatMasker. Would that cause it? I’m happy to send along whatever data files you’d find useful to reproduce the issue.
> 
> Cheers,
> Shaun
> 
> ##gff-version 3
> 17    barrnap:0.5    rRNA    130358    131272    .    -    .    Name=16S_rRNA;product=16S ribosomal RNA (partial);note=aligned only 57 percent of the 16S ribosomal RNA
> 18    barrnap:0.5    rRNA    6238    7489    .    -    .    Name=12S_rRNA;product=12S ribosomal RNA
> 5    barrnap:0.5    rRNA    7    1246    .    -    .    Name=12S_rRNA;product=12S ribosomal RNA
> 6    barrnap:0.5    rRNA    449193    450443    .    +    .    Name=12S_rRNA;product=12S ribosomal RNA
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