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How do I upload a gff file?

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".  However, more complex GFFs exist and require more sophisticated sorting to be displayed. In these cases, gff3sort is a very useful tool.
  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. Select the correct "Genome" for your use in the top left.
  5. Select "Tracks" in the top left
    1. Under "Local files", click "Select Files" to get your local gff file and index.  
    2. Once your files are selected, click "Open" and it should display.

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 structures in Jbrowse. Your gff file output should look similar to the "DNA Transposons" track below.

Screenshot of gff file output in Jbrowse