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
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
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