Abstract
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’s precise splice detection achieves high accuracy on simulated data, improves concordance between matched single-cell and bulk datasets, increases agreement between biological replicates, and reliably detects un-annotated splicing in single cells, enabling the discovery of novel splicing regulation.
Competing Interest Statement
The authors have declared no competing interest.
Copyright
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