About GFF validation

Question

[iraun]

Hi all,

I've just created a new GFF off a new version of a genome X using liftOver tool. I would like to know any method to 'validate' this new GFF. I'm going to use 'eval' tool ( http://www.biomedcentral.com/1471-2105/4/50 ) to get some statistics about the new annotation, and I'm thinking about extracting transcript sequences from both GFF (old and new), and blast them against each other to see the length of the alignment, see the differences between both versions...etc.

If anyone has done this kind of analysis (or if anyone has any idea about this), I would like to hear new opinions/suggestions.

Thanks :)

[Istvan Albert]

Don't delete questions that have answers - it is not a nice practice - basically you take away someone else's ability to gain information after you yourself have been helped. Yes I agree that it is not a good question - but that too can help someone else later will understand how to ask a better question

[iraun]

Sorry Istvan. I never delete the posted questions because of the reason you mentioned, but, in this particular case I thought that there was nothing to learn from here. I have not thought that this question might be a clear example of how to make a bad question :P.

Thanks again.

[Malcolm.Cook]

This is a duplicate of A: How to verify the information stored in a GFF file

Answer 1

[Istvan Albert]

You seem to use the GFF and GTF interchangeably. So it is not clear if you have a GFF file or a GTF file.

You can validate GFF files here: http://genometools.org/cgi-bin/gff3validator.cgi

Some tips to validating GTF files: Gtf2.2 Validation And Conversion

[iraun]

Sorry my mistake, actually I have a GFF file. I'm looking for a way to compare the old gff with the new one. See if the genes have changed, new transcripts... The tools you mentioned are tools for validate the GFF format, not the "content" of the new annotation... Maybe my post is a little confusing.

[Istvan Albert]

ok I see, this has nothing to do with GFF validation, what you want is to verify some type of information you found that happens to be stored in a GFF. I would suggest reposting the whole question with a different title and content and de-emphasizing the format