How do I upload a bed file?

Frequently Asked Questions
Question: 

With all of the possible formats to a bed file, what is the easiest mechanism to upload a bed file that is viewable in Jbrowse?

Answer: 

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.  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 fourth column in your bed file, the Jbrowse display may be finicky.  Your bed file output will look similar to the "80 Effector MEME -> FIMO motifs" track below.

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