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Question: Validator for GFF?
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gravatar for Susanne Warrenfeltz
4.4 years ago by
Susanne Warrenfeltz • 40
United States
Susanne Warrenfeltz • 40 wrote:

Hello

I am trying to use/visualize a GFF file from ToxoDB in Galaxy.  The file passes the validator (link below) but is not recognized by Galaxy as a GFF file.  Do you have a preferred  GFF validator that will help me correct the my file format so that it is used by your trackster?

http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

Thanks

Susanne
gff • 1.2k views
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modified 4.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.4 years ago by Susanne Warrenfeltz • 40
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gravatar for Jennifer Hillman Jackson
4.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is a good validator. And the file appears to be fine from my checks. Here is what we have in our wiki for reference (also points to GMOD): 
http://wiki.galaxyproject.org/Learn/Datatypes#GFF3

The file name ending with a "gff" instead of a "gff3" is what is throwing off the auto-detection (and triggering the default to bed). You can either pick "gff3" as the datatype from the menu at upload (instead of auto-detect), or re-assign the datatype after upload (Click the pencil icon to reach the Edit Attributes form. In the center panel, using tabs to navigate, change the datatype [3rd tab] and save). I loaded it both ways using the URLs directly from the web site. For both a gff3 file and a fasta file for the same genome. 

The fasta file can be used to create a "Custom Build" (User menu -> Custom Build). Assign that as the database to the GFF3 file (on the Edit Attributes form [1st tab] and save), then launch Trackster. This may take a bit to process, so save it (upper right corner disk icon), then come back after a while and check if done. More tracks can be added, if mapped to this same genomic reference.

Best, Jen, Galaxy team

 
ADD COMMENT • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k
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