How to represent trans-spliced genes in GTF?
For example, see this gene (nad1) in ENA: http://www.ebi.ac.uk/ena/data/view/ABI60879
If you look at the XML for that gene you see the following:
join(
DQ984518.1: 324706 .. 325091 ,
complement(DQ984518.1: 24417 .. 24498),
complement(DQ984518.1: 22828 .. 23019),
DQ984518.1: 3484 .. 3542 ,
complement(DQ984518.1: 153702 .. 153960)
)
Which shows 5 exons joined out of phase and out of order. Is there a valid GTF representation of this?
How to dump a 'non-canonically spliced' gene into GTF? i.e. what's the recommendation?
1 answer
GTF is a very simplistic and ill-defined format - it is a variant of GFF 2 that only has two required fields
gene_id "ABC"; transcript_id "EFG";
beyond that, there is no requirement. So I don't think it could be turned into a "standard" GTF form since that, in turn, does not exist.
Perhaps as Devon Ryan points out you may use GFF3 with multiple parents.
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Istvan Albert
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Also, how to verify that the resulting GTF is valid? Compare the translation?
Hello Dan!
It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/849/how-to-represent-trans-spliced-genes-in-gtf/855#855
This is typically not recommended as it runs the risk of annoying people in both communities.