Question: Merging 2 GFF files
gravatar for bwczech
10 weeks ago by
bwczech60 wrote:


I have combined two gff files for my annotation. One GFF represents chromosomes 1-29 + X and second GFF represents Y chromosome. The same situation is with genome (I have combined two genomes for my purposes).

The problem is with ID and Parent field in GFF because they are overlapping. I mean Y chromosome has the same ID as 29 chromosome:

Y   Gnomon  gene    2502499 2571410 .   +   .   ID=gene32386;Dbxref=GeneID:100849399;Name=LOC100849399;gbkey=Gene;gene=LOC100849399;gene_biotype=protein_coding

and the same ID (gene32386) here:

29  Gnomon  pseudogene  37912602    37922321    .   -   .   ID=gene32386;Dbxref=GeneID:615840;Name=LOC615840;gbkey=Gene;gene=LOC615840;gene_biotype=pseudogene;pseudo=true

How can I fix that problem? Because of that situation I cannot do annotation of my Y chromosome. Should I modify ID and Parent field in my GFF or what?

merge combine gff gff3 • 163 views
ADD COMMENTlink written 10 weeks ago by bwczech60

Should I modify ID

That would work, I suppose.

ADD REPLYlink written 10 weeks ago by WouterDeCoster36k

But the ID modification will not impply for results of snpEff annotation? How should I modify ID? Changing the NUMBER or I can just add extra char?

ADD REPLYlink written 10 weeks ago by bwczech60

Adding extra character is enough and probably the easiest. If you have already done downstream analysis with snpEff I don't know what it might imply. If it was using the IDs I guess it would have complain to meet duplicate IDs.

ADD REPLYlink written 10 weeks ago by Juke-341.8k
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