How do I upload a gff file?

Frequently Asked Questions
Question: 

With thousands of formats possible in a gff, what is the easiest method to upload a gff file that is viewable in Jbrowse?

Answer: 

Tabix is a program that is necessary to be able to index the gff file for upload and display in Jbrowse.  However, getting a gff file viewable in jbrowse is a little more work than a bed file. 

1. Sort your gff file by scaffold name and position.  Typically this works like "sort -k1,1V -k4,5n file.gff >sorted_file.gff"

2.  Zip your file with bgzip.  As simple as "bgzip sorted_file.gff"

3.  Index your zipped file with tabix.  "tabix -p gff sorted_file.gff.gz"

4.  Log in to SCNbase.org, go to content at the top left, then add content, then downloadable file.

5. Be ready to add the required info (Title, Organism, very basic pipeline/methods/program versions, and the source of the data).  Make sure to click, "Expose as Jbrowse track".

Be aware that your scaffold names must match the Jbrowse scaffold names in every respect (capitalization, underscores, numbering, etc).  If you have a ninth column in your gff file, the "ID=" must be present in the ninth column for any names to be attached to the coordinate in Jbrowse.  Your gff file output will look similar to the "DNA Transposons" track below.

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