Adding Cuffdiff support to IGV

[craigb]

I'm looking to add direct support for an RNA-Seq pipeline (Tophat->Cufflinks->Cuffdiff) to the IGV genome browser so would be interested in getting some input from you guys about which of the output files you want to visualise and how.

IGV already supports bam and gtf files, as well as expr - although as far as I can tell Cufflinks no longer outputs expr files (please correct me if I'm wrong). It also handles expression data in the form of gct/res files which it displays as a heatmap by default. So given a Cuff* pipeline also produces a lot of diff and fpkm_tracking files I'm looking to add that support into IGV so they can be loaded directly.

So I'd be interested in hearing what approaches are currently being taken with these files to help visualise the data (if at all - obviously I'd quite like to know if I'm just wasting my time if there's no point in loading them into something like a genome browser).

Let me know your thoughts here or reply to me off list if you'd like to be involved with this project.

TIA

[jbrwn]

i'd definitely like to see support for these file types, but they would need to be handled like igv handles tdf or bam files.

what i have now is a simple bar graph per gene showing each of the transcripts groups by transcription start site. i provide the researcher a url to launch an igv session with truncated transcript.gtf for each subject, coverage, refseq reference, and ensembl reference. the gtfs have to be truncated because they load entirely into memory and will cause igv to crash if the computer runs out of ram. having to truncate the files means the researcher will have to launch a new igv session for each gene of interest since igv's "new session" doesn't clear any tracks and kills the gui.

personally, i would like to see more external control options. something to update the data file by track name, remove a track, successfully start a new session, successfully load a saved session overwriting any previous session, etc. i'd be happy to discuss more or clarify anything i said in this ramble.