Yang I. Li1, David A. Knowles1, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard

1Equal contribution

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

  • easy detection of novel introns
  • modeling of more complex splicing events than exonic PSI
  • avoiding the challenge of isoform abundance estimation
  • simple, computationally efficient algorithms scaling to 100s or even 1000s of samples

For details please see our bioRxiv preprint

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