I have raw count of isform expression levels and I would like to do differential isform expression analysis between two different conditions.
Does any of you know about tool that do DE isoform calling?
Isoform inference is not straight forward, but is implemented in the cufflinks package.
It's rather hard to distinguish to which transcript reads belong with short reads.
More straightforward is to count on the exon level, less ambiguous. This you can do using DEXSeq
Depends on how you obtained your "raw isoform counts". If you have a very simple experiment, and I mean 2 groups to compare against, then Kallisto -> Sleuth is the most straightforward was to achieve what you want. Sleuth is however an absolute pain if you have a more complex design than two groups, there seems to be no support for contrast matrices like you'd see in Limma, or ways of interrogating your model fit with flexibility, like DESeq2.
I agree fanli.gcb, there are no perfect method to perform isoform quantification and differential expression. But there are studies uses available methods to perform the task. There is also a recent study where they used similar approach as I described in previous post using MISO,