Is there a way to create a track based on FPKM values of RNA-seq data and load that in IGV along with the alignments? Specifically, if a region is diff. expressed from RNA-seq data, I'd like to visualize that in IGV with the FPKM values (just raw alignment depth could be misleading as it is not normalized). Is bedgraph an option for this?
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written
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learnerforever
2 answers
I'd check out:
http://www.broadinstitute.org/igv/RecommendedFileFormats
You might want to consider changing your data to BED or GCT. I'm not sure that you need bedGraph since you will have only one value per gene/transcript.
You might consider using the Savant Genome Browser. Savant includes an optional Cufflinks Plugin. You may also want to take a look at this thread: How to interpret Cufflinks results
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FPKM (or RPKM) values are single values for whole gene. And IGV shows normal count based coverage plots (which could be altered with your own file). So, I'd create a uniform coverage with FPKM value over the length of the gene (over the exons if its RNA-Seq) and input it separately.