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Specific splice junction detection in single cells with SICILIAN.

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 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.

SUBMITTER: Dehghannasiri R

PROVIDER: S-EPMC8339681 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature

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Specific splice junction detection in single cells with SICILIAN.

Dehghannasiri Roozbeh R Olivieri Julia Eve JE Damljanovic Ana A Salzman Julia J

Genome biology 20210805 1

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 ...[more]

PMID: 34353340

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