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How do I upload a bed file?

Tabix is a program that is necessary to be able to index the bed file for upload and display in Jbrowse.  Once this program is installed, the process is fairly easy.

  1. Sort your bed file by scaffold name and position.  Typically this works like "sort -k1,1V -k2,2n bedfile.bed >sorted_bedfile.bed"
  2. Zip your file with bgzip.  As simple as "bgzip sorted_bedfile.bed"
  3. Index your zipped file with tabix.  "tabix -p bed sorted_bedfile.bed.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 bam 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 fourth column in your bed file, the JBrowse display may be finicky.  Your bed file output will look similar to the "Ribosomal Genes" and "Tandem Repeats Finder" tracks below.

JBrowse Display