Best way of visualzing RNA-seq bam files

Question

[ATRX]

I have about 100 bam files from a time course experiment. I am interested in knowing the best way to visualize the bam files on IGV esp investigating the splicing changes. Since these files are on the hpc server, and cannot be downloaded & loaded on the IGV app on my mac computer, is there a way where I can make the files public and visualized on the IGV? Thanks!

Answer 1

[GenoMax]

IGV can be installed on the server and display projected back to your Mac via X11. It may be a bit clunky and will require good network connectivity.

But if you envision making the files available "public" (in perhaps some limited context e.g. inside your institution) then you could also make use of "load from URL" feature: https://igv.org/doc/desktop/#UserGuide/loading_data/#loading-tracks by putting the files up on a web location/AWS.

[ATRX]

Awesome, thanks!

Answer 2

[LChart]

If your network connectivity is poor, I have had very good success with running IGV.js (https://github.com/igvteam/igv.js/) on a remote machine, and port-forwarding via ssh. This keeps the data rendering on the server and is super-helpful over a crappy VPN connection (like on a plane)

[ATRX]

this is helpful. thanks!