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Question: How to define several regions in GFF3 file?
Entering edit mode

Dear all,

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

##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.

Entering edit mode

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

##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
ADD COMMENTlink 10 months ago Juke-34 ♦ 2.2k
Entering edit mode

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

ADD REPLYlink 10 months ago
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