Question: How to Run IGV on Linux Remote Machine
0
gravatar for Aynur
6 weeks ago by
Aynur40
Aynur40 wrote:

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, 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.

sequencing rna-seq alignment • 171 views
ADD COMMENTlink modified 6 weeks ago by i.sudbery11k • written 6 weeks ago by Aynur40
1

you can use an SSH-X11 forwarding or use a VNC session to run IGV on your remote machine

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by JC12k
1

Can I visualize this directly on remote computer ?

All the solutions mentioned below will work only if you have reasonably good internet connectivity (speed wise). If you are having problems downloading data because of bandwidth then YMMV with the solutions mentioned below.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by GenoMax96k

If you can SSH to the remote machine, you could use sshfs to mount the remote filesystem and have IGV read from it. See: IGV over SSH?

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Ram32k

Yes, I do use ssh . I will check this out. Thanks.

ADD REPLYlink written 6 weeks ago by Aynur40
3
gravatar for i.sudbery
6 weeks ago by
i.sudbery11k
Sheffield, UK
i.sudbery11k wrote:

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 server is popular as a standalone solution and mobaXterm integrates a terminal and ssh solution.

In OSX you'll need to install XQuartz.

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 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.

ADD COMMENTlink written 6 weeks ago by i.sudbery11k

Thank you very much for detailed answer. I am sorry to ask again, but is it ok I already downloaded commandline ivg for my remote machine or do I need to download it for linux specifically?

Thank you.

ADD REPLYlink written 6 weeks ago by Aynur40
1

Just a note: It's IGV (Integrative Genomics Viewer), not IVG. I noticed you misspellled it a bunch of times in the question too, which I fixed earlier.

ADD REPLYlink written 6 weeks ago by Ram32k
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