Question: Validator for GFF?
gravatar for Susanne Warrenfeltz
4.4 years ago by
United States
Susanne Warrenfeltz40 wrote:


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?



gff • 1.2k views
ADD COMMENTlink modified 4.4 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by Susanne Warrenfeltz40
gravatar for Jennifer Hillman Jackson
4.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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):

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 COMMENTlink written 4.4 years ago by Jennifer Hillman Jackson25k
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