Question: Gtf2.2 Validation And Conversion
1
gravatar for Pi
9.7 years ago by
Pi520
Pi520 wrote:

Greetings

Can anyone recommend a GTF2.2 validator? There is a link to one on this page but linked page doesn't appear to be working. There is also another validator here but there isn't a readme file so I don't know if it is validating GTF2.2 or earlier version of the file format.

Also on the GTF2.2 page given above it says in the title that GTF2.2 is revised ensembl GTF. Does that mean that ensembl GTF downloads are not valid GTF2.2. If not, is there a means of converting ensembl GTF to GTF2.2. This biostar question here contains a comment which suggests ensembl GTF is GTF2.2

Edit: in response to Brad's comment I want to use GTF2.2 because I am using PLINK/SEQ and the custom annotation databases used by that are imported in GTF2.2 format.

thank you for your time

gtf conversion • 3.1k views
ADD COMMENTlink modified 7.5 years ago by Biostar ♦♦ 20 • written 9.7 years ago by Pi520
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Could you add some details about what are you trying to do with GTF2.2? It's not that well defined with tons of variants which is why GFF3 was developed: http://www.sequenceontology.org/gff3.shtml. You should use GFF3 if you are creating new files. If you want to parse Ensembl files, I have a Python parser that reads all of the various GFF/GTF versions: http://biopython.org/wiki/GFF_Parsing

ADD REPLYlink written 9.7 years ago by Brad Chapman9.5k

So you are using Ensembl GTF annotations with plink? I don't have any experience with this, but maybe if you report the error or problem you are seeing someone could identify something. For your general question, you may have a hard time finding current GTF2.2 resources since it is not the latest recommended specification.

ADD REPLYlink written 9.7 years ago by Brad Chapman9.5k
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