What can I do with RNA-seq RPKM exon level data ?

Question

[avari]

Hi all,

I am new to RNA-seq. I want to learn about RPKM and what you can do with it, however I am finding the online resources hard to navigate so far. Specifically I want to know if I can look at alternative transcript usage using exon level RPKM, is this possible without access to the raw data (I just have RPKM counts per exon and RPKM counts per gene) ?

Thanks!

Answer 1

[Istvan Albert]

It depends on what type of alternative splicing the gene in question has.

Without access to the splice junctions (from the alignment file) we can't identify which exons belong together. On the other hand there may be transcripts uniquely characterized by a single exon in which case you may be able to infer which transcript is present.

[avari]

Thanks a lot for the useful information! Unfortunately I suspected as much. I am now considering looking at differential exon usage instead. From reading this paper it seems as if that is possible without necessarily having the raw data: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460195/