Specific splice junction detection in single cells with SICILIAN

Genome Biol. 2021 Aug 5;22(1):219. doi: 10.1186/s13059-021-02434-8.


Precise splice junction calls are currently unavailable in scRNA-seq pipelines such as the 10x Chromium platform but are critical for understanding single-cell biology. Here, we introduce SICILIAN, a new method that assigns statistical confidence to splice junctions from a spliced aligner to improve precision. SICILIAN is a general method that can be applied to bulk or single-cell data, but has particular utility for single-cell analysis due to that data's unique challenges and opportunities for discovery. SICILIAN's precise splice detection achieves high accuracy on simulated data, improves concordance between matched single-cell and bulk datasets, and increases agreement between biological replicates. SICILIAN detects unannotated splicing in single cells, enabling the discovery of novel splicing regulation through single-cell analysis workflows.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Alternative Splicing
  • Animals
  • Computational Biology / methods
  • Entropy
  • Humans
  • Mice
  • RNA Splicing*
  • Sequence Analysis, RNA / methods
  • Single-Cell Analysis*