What are the best options for Isoform Switching Analysis in R?

Question

[Trivas]

I've been following the vignette for IsoformSwitchAnalysis but I gotta say, it feels like it's more hassle than it's worth. For starters, there are so many typos in the vignette and function options that I've had to start working in an IDE rather than on my AWS instance to try and catch errors. Additionally, there are so many external programs that need to be run with the results fed into the package for downstream analyses. This is generally fine, except the output of these programs don't match what the package expects, causing me to reformat all of the outputs. And some of them (pfam) have a 6 hour or longer wait time to email results.

Does anyone have suggestions for other pipelines to use? I want to take a look at alternative splicing and quantify differential isoform usage. Very exploratory analysis for now with no defined end goal.

Answer 1

[i.sudbery]

For differential transcript usage, the three approaches we have used are DEXseq, DRUM and Swish (from fishpond). All three require quantification with Salmon before going ahead with the statistical analysis. DEXSeq and DRUM are the engines behind IsoformSwitchAnalyzeR. The trick with DEXSeq is that while the manual and vignette for DEXseq reffers to using the quantification of exons, you use the quantification of transcripts. Swish is a relatively new appraoch that makes use of the inferenctial uncertainty.

For alternative splicing analysis (as opposed to differential transcript usage) - that is event level analysis rather than isoform level analysis, we have used rMATS and, again, DEXSeq (this time using exon counts or junction counts).