Hello everyone, I'm looking for a script or a tool able to merge two gff3 files, made as follows:
1) A file containing annotation data for my species
2) Another file with additional annotation (information obtained later, trying to annotate the genome against another organism in order to give a function to more genes)
The coordinate system of the two gff3s is the same since both the gff3s are produced starting from the genome of my species of interest.
Anything I found seems to be outdated, thanks in advance for your help!
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written
by
Raito92
1 answer
I use AGAT for that and many other GFF processing things as well.
depends on what exactly you want to achieve but yes, agat_sp_merge_annotations.pl sounds about right.
alternatively you can first cat both gff files together and then run agat_convert_sp_gxf2gxf.pl to fix the 'issues' .
On their github page there are lots of explanations and guidelines on what to use when. There are likely also different routes that lead to the same result.
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