Hello, 

I am doing mouse RNA-Seq analysis. I want to visualize mapped bam file on IGV. I am having hard time downloading my bam files from linux remote machine to local computer. Can I visualize this directly on remote computer ? 

I tried to read user guide from [IGV][1], but I still could not figure out how to run my commands ?

If you can recommend me any tutorials, I greatly appreciate it.

Thank you very much. 


  [1]: https://igv.org/
There are three ways to do this:

1. X forwarding
2. Remote Desktop
3. Mount the remote machine as a network share on the local machine. 

In both the first two cases you need to install IGV of the remote linux machine. Older version are available from most of the main linux repos, so you should be able to install with something like `apt-get install igv` or `yum install igv`. Alternatively if you use the (ana)conda package management system on the remote machine, you can install a recent version with `conda install igv -c bioconda`. 

# X forwarding

If you are using Windows or OSX on the local machine  you will need to install an X server on your local machine. There are several windows X11 servers, that are either intergrated with terminal emulators or stand alone. The [VcXsrv][1] server is popular as a standalone solution and [mobaXterm][2] integrates a terminal and ssh solution. 

In OSX you'll need to install [XQuartz][3].

Now connect to your remote server with your favourite SSH solution making sure you configure it to forward X11 connections. On the commnad line thats `ssh -X`. Start IGV on the remote machine and if your X Server is correctly configured, IGV will appear on your local machine. 

# Remote Desktop
If the remote machine is a desktop linux machine, you should be able to run a remote desktop sharing daemon on it and then connect to that remote desktop from the local machine. I've successfully used [Chrome Remote Desktop][4] for this, but many other solutions exist.

# Mount the remote machine on the local machine

Basically in this solution you make the disk of the remote machine appear like a network drive on the local machine. The most fail safe way to do this is using `sshfs`, which use can use to connect to any machine that will accept incoming ssh connections. 


  [1]: https://sourceforge.net/projects/vcxsrv/
  [2]: https://mobaxterm.mobatek.net/download.html
  [3]: https://www.xquartz.org/
  [4]: https://remotedesktop.google.com/headless/