How do I get a bam file uploaded to SCNbase.org and have it publicly viewable in Jbrowse?
First thing to consider, is your bam file larger than 10Gb? 10Gb is the maximum allowable file size to upload to SCNbase, and thus you will not be able to make it publicly available. However, files that are larger than 10Gb can be viewed by directly uploading them to Jbrowse, rather than SCNbase.
1. Map your reads to the genome. Make sure it is the correct version of the genome found here on SCNbase.org, "genome738sl.polished.mitoFixed.fa"
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. Log in to SCNbase.org, go to content at the top left, then add content, then downloadable file.
6. 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).
The bam output in Jbrowse gives you something like the below output, assuming your alignment is rna-seq.