Tag: splicing

A working guide to quantifying transcript isoforms from short-read RNA-seq: building a Salmon index, running selective alignment, importing with tximport, testing differential transcript usage with DRIMSeq and DEXSeq, and deciding when the answer requires long reads.

A working pipeline for going from RNA-seq FASTQs to junction counts, PSI values, and a shortlist of splice-altering variants from your own genome, with the tools and parameters we would use.