Is there a way to view wiggle/bigWig in terminal

[feeldead]

Undoubtedly, there are many viewers UCSC Genome Browser, IGV, IGV, .... However, if you ssh to a remote server and want to take a quick view of the data, view large datasets on a traditional viewer is too much. Is there a way to view them in the terminal? In other words, is there a terminal version of genome browser?

[apredeus]

well that's kind of an oxymoron don't you think? Terminal implies no graphics. You don't really mean "visualizing genome with ASCII symbols" do you? Because that would be quite a project.

I understand the problem though. There are few things you can do.

One, you can extract regions of interest and only download those.
Two, you can develop certain metrics (or use existing ones) and get the information about the file without the visualization. Think about what are you looking for.
Three, you can take bed files with called peaks. Those are usually fairly small and you can download them quickly. Also, you can use igvtools, make a coarse-grained .tdf file and download that one - if you choose the parameters right, it can be as small as 10Mb.

Hope this helps.

[kadircaner]

I dont know whether it will be useful for your case but check this regarding extracting regions from wig files on a remote server:

http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database

[dariober]

Undoubtedly, there are many viewers UCSC Genome Browser, IGV, IGV, .... However, if you ssh to a remote server and want to take a quick view of the data, view large datasets on a traditional viewer is too much. Is there a way to view them in the terminal? In other words, is there a terminal version of genome browser?

Hi- Have you considered samtools tview? It works with sam/bam files so you would need to convert your input to this format.

Alternatively, you could install IGV on the remote host (where the big files are) and ssh to it with the -X flag to forward the graphical interface to your local machine.

Hope this helps...

Dario