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no gene_id for tRNA in GFF3

Hi,

In one of the non-human organisms, GFF3 annotation file downloaded from NCBI genome FTP, there were some tRNA annotations (tRNA-Glu, tRNA-Ser, etc) in the mitochondrial genome that did not have a gene_id. They don't have any transcript features associated with them as well. Is it a usual annotation issue in the GFF3 format or by practice tRNA genes don't have either gene_id or transcripts associated with them?

The problem is that when the GFF3 is converted to GTF using gffread, no gene_id is present for those tRNAs and hence creating downstream issues. Should they be removed altogether if we are not exclusively interested in them?

annotation gff3 gtf
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written by prasundutta87 prasundutta87

2 answers

GFF(3) is the worst 'standard' , so yes unfortunately all different flavors and values being present or not can occur in a gff3 file.

I must add that the tRNAs (well all non mRNAs actually) is a bit of a grey zone, some will add the gene_id or even transcript to them and other providers will not

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written by lieven.sterck lieven.sterck

Hmm..ok..so its better to just drop them off in our case.

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written by prasundutta87 prasundutta87

if you're not interested in them , sure you can omit them

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written by lieven.sterck lieven.sterck

I was also thinking of an option to give dummy gene and transcript IDs to them.. but haven't done that yet..can that be a workaround as well?

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written by prasundutta87 prasundutta87

that's an alternative indeed. if you don't really need them you can 'fix' your gff file until it's valid

or perhaps use the gffvalidator which can try to fix some errors

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written by lieven.sterck lieven.sterck

Thanks a lot Lieven! This was very helpful.

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written by prasundutta87 prasundutta87

you're welcome!

if this has resolved your issue would you mind flagging this one as 'solved'? (probably need to convert one of the posts as an answer though)

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written by lieven.sterck lieven.sterck

I could only moderate my post to make it as an 'answer'..the main answer should be your first reply..

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written by prasundutta87 prasundutta87

right, indeed, only I can move my own posts up.

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written by lieven.sterck lieven.sterck

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