from dexseq results to alternative splicing events identification
Hello everyone
I have transcript abundance data from salmon for 24 samples. I followed https://bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html#salmon-quantification workflow for the DTU quantification. I have got result from DRIMSeq, DEXSeq which shows the transcript usage across the samples. Next, I would like to further identify different types of alternative splicing i.e intron retention, mutually exclusive exons etc. Which method would be suitable to go further ? I would appreciate all the suggestion.
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You could try the IsoformSwitchAnalyzeR package, it works with DEX/DRIMSeq.
Thanks alot.