How do I upload a bam file?

While there is a 10Gb limit to files that can be hosted on SCNBase, there is no limit on how large a bam file can be to be displayed in JBrowse.  

1. Map your reads to the genome. Make sure it is the correct version of the genome found here on SCNbase.org,
2. Convert your sam file to a bam file (Can be done with "samtools view -bS file.sam >file.bam")
3. Sort your bam file  (samtools sort file >sorted_file.bam)
4. Index your bam file (samtools index sorted_file.bam)
5. Select the correct "Genome" for your use in the top left.
6. 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).

The bam output in Jbrowse gives you something like the below output, assuming your alignment is rna-seq.