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no gene_id for tRNA in GFF3
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14 months ago
prasundutta87 • 330

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?

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4 months ago
VIB, Ghent, Belgium

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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14 months ago
prasundutta87 • 330

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

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

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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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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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Thanks a lot Lieven! This was very helpful.

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

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

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