LeafCutter: Annotation-free quantification of RNA splicing.
Yang I Li, David A Knowles, Jonathan K Pritchard.
For details please see http://biorxiv.org/content/early/2016/03/16/044107
To compile the R package to perform differential splicing analysis and make junction plots:
cd leafcutter
R CMD INSTALL --build .
Note you'll need the following R packages: rstan, foreach, ggplot2, R.utils, gridExtra, reshape2, Hmisc, dplyr, doMC, optparse.
For a (hopefully) complete example of the complete pipeline, take a look at
example_data/worked_out_example.sh