Question: How to validate GFF3?
1
gravatar for mike.thon
3.8 years ago by
mike.thon30
Spain
mike.thon30 wrote:

What tools are available to validate a GFF3 format file? I tried the one recommended by the Sequence Ontology Project but it has been offline every time I try it. I also tried GenomeTools. It helps but it does not catch all of the errors.

gff • 1.6k views
ADD COMMENTlink modified 3.6 years ago by rmf760 • written 3.8 years ago by mike.thon30
2

You may want to state what your purpose is (or the problem you are having) because different tools have slightly different definitions of what "valid" means.

ADD REPLYlink written 3.8 years ago by SES8.2k
1

htseq hasĀ  GFF_Reader method, which parse a GFF file.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by geek_y10k
1
gravatar for igor
3.8 years ago by
igor8.9k
United States
igor8.9k wrote:

What about GFF tools?

http://www.raetschlab.org/suppl/gff-tools

ADD COMMENTlink written 3.8 years ago by igor8.9k
1
gravatar for rmf
3.6 years ago by
rmf760
rmf760 wrote:

gff3validator from genometools? http://www.genometools.org/cgi-bin/gff3validator.cgi online web version and commandline tool.

ADD COMMENTlink written 3.6 years ago by rmf760
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