splicingrates

CODE FOR PAI et al 2018 eLIFE

1. Simulations to assess approachs to calculate rates of intron splicing from nascent 4sU-seq data (to be run over various parameters as inputs)

   get reads/value for all 3 methods: simulation.R
   simulation of PSI decrease method (inputs of MISO summary PSI values run with output from simulation.R): miso_modeling.R
   simulation of junction dynamics method (inputs are output from simulation.R): junction_modeling.R
   

2. Code to calculate and analyze mRNA splicing rates from Drosophila 4sU-seq data

   SplicingRates.Rmd

3. Code to recreate figures in Pai et al. 2018

   SplicingRates_figures.R