JBrowse on GitHub (A question about file size)

Question

[I0110]

Hi,

I was asked to make a JBrowse for our RNA-seq data. I found a POST about how to do this with GitHub and Netlify. However, the GitHub file size limit is only 25MB. How do we include the sequencing result files that are usually few GB on GitHub? What are the alternatives that people typically use when setting up JBrowse? Thanks a lot!

[GenoMax]

Tagging: cmdcolin

[cmdcolin]

Thanks for the tag:)

Answer 1

[cmdcolin]

Files for JBrowse tracks e.g. bam, bigwig, etc can be hosted on basically any file server, but I'm not aware of what free options are available for large files. For a small cost, Amazon cloud services like aws s3 is one option. You could host the jbrowse instance on aws s3 alongside the bam, bigwig etc (jbrowse is just static JS and HTML files and can be stored on s3) or host jbrowse on GitHub pages and point at track data hosted on s3 in the url (your s3 bucket will need to have CORS enabled in that case so the cross origin access of data will work). The other option commonly is if your university has a web server of their own, you can host it using a normal apache server for example, but certainly cloud options like s3 are common for labs now

[I0110]

Thanks so much cmdcolin! I will try to host a JBrowse instance on AWS S3.