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
0 answers
No answers yet.
Log in to answer this question.
-
How to select specific values (features and attributes) from gtf/gff file and convert it into table…
written by kirannbishwa01
-
Where can I download the GTF2.2 format file for mm10?
written by Gjain
-
Gtf Format End Coord Included Or Excluded
written by vodka
-
'What Scholarships Are Available In The Uk'.
written by Ammu •
-
Can Bam File Be Converted To Fasta Format?
written by Hmm •
-
Are Snps Frequencies Between Individuals Or Chromosomes
written by Pi •
-
Functional Annotation Of Pathways
written by Pi •
-
Difference Between Coverage And Read Depth ?
written by Monzoor •
-
Short Read Aligners/ Snp Calling Comparison
written by Pierre Lindenbaum
-
System Commands For Alignment Viewer In Php
written by Aparna •
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
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.