Opened 12 years ago

Last modified 8 years ago

#188 new task

Add IGV as an extension similarly to MEV

Reported by: base Owned by: Jari Häkkinen
Priority: major Milestone: ZZ A wish list
Component: not classified Keywords:
Cc:

Description

The IGV tool found at http://www.broad.mit.edu/igv/index.html is a neat java web start program used for visualization and exploration of genomic data. It is designed to handle different types of data which enables simultaneous visualization of e.g. gene expression and gene copy numbers for the same set of tumors. Also, one can import a sample annotation file for sorting and filtering of the data to be displayed.

The simplest way for this to work is to be able to export pre-defined file formats from BASE and make IGV as a clickable extension in the analysis tree.

Is this something that the BASE team can do?

Change History (4)

comment:1 Changed 12 years ago by Nicklas Nordborg

What license is IGV distributed under. I can't find anything on their home page and I can't find any source code either. This makes me think that it is not a GPL-compatible program. Anyone with information on this?

comment:2 Changed 12 years ago by Peter Johansson

The source can be found under Downloads; you need to register though.

Everything is under GPLv2 except some 3rd party pkgs which are under other free licenses.

comment:3 Changed 12 years ago by Nicklas Nordborg

I have downloaded IGV but I have absolutely no clue what to do. Ok, I can load the example data files found on their download page, and I get a "colorful" display. I have however no idea what is needed for BASE to produce a file that IGV can read. I tried feeding it a MeV TDMS file. No error message but it didn't display anything that was similar to the example data. I guess it means that a new export file format is needed. It would be nice with contributions in this area from users of the IGV application. We can provide space in our code repository for such a project.

comment:4 Changed 8 years ago by Jari Häkkinen

Milestone: A wish list
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