Yang I. Li1, David A. Knowles1, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) intron usage across samples. The advantages of this approach include
For details please see our bioRxiv preprint and corresponding Nature Genetics publication.
Additionally, for full details on the leafcutter for Mendelian Diseases (leafcutterMD) method that performs outlier splicing detection, see our Bioinformatics publication.
Check out a demo leafcutter shiny app here: 10 brain vs. 10 heart samples from GTEx.
We have a Google group for user questions at https://groups.google.com/forum/#!forum/leafcutter-users