How to define several regions in GFF3 file?

Question

[marongiu.luigi]

Dear all,

I am trying to customize a GFF3 file containing features from two distinct genomes. I created the lines:

##gff-version3
##sequence-region custom 1 278541

The length of the feature is the combination of the two individual genomes. I set each genome as a different region, thus I have the lines (3 and 436, respectively):

NC_<something> Genebank region 1 147589 . + . ID=<custom>;Name=<something>
...
NC_<something_else> Genebank region 147590 278541 . + . ID=<custom>;Name=<something_else>

I then ran gff3validator from the gt package but I got:

$ gt gff3validator <file>.gff3
gt gff3validator: error: the multi-feature with ID "<custom>" on line 436 in file "<file>.gff3" has a different sequence id than its counterpart on line 3

Since the ID is <custom> in both cases, the difference is in the names not the IDs. Or should the NC_<something> and NC_<something_else> be the same?

What I am missing?

Thank you.

Answer 1

[Juke34]

I guess the ID has to be uniq here, I would try something like that:

##gff-version3
##sequence-region custom 1 278541
NC_something Genebank region 1 147589 . + . ID=Id1;Name=something
...
NC_something_else Genebank region 147590 278541 . + . ID=id2;Name=something_else

[marongiu.luigi]

Yep, I think you are right: the ID needs to be unique even for the different regions. Thanks.