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Updated: May 9, 2026

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

SCOTCH: isoform-level characterization of gene expression through long-read single-cell RNA sequencing.

Zhuoran Xu^1,2, Hui-Qi Qu³, Joe Chan²

¹Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA.

Nature Communications

|May 7, 2026

Summary

SCOTCH is a new pipeline for analyzing long-read single-cell RNA sequencing data. It accurately characterizes full-length isoforms and identifies novel transcripts across various platforms.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Long-read single-cell RNA sequencing (lr-scRNA-Seq) allows for full-length isoform profiling at the single-cell level.
Accurate isoform characterization is crucial for understanding cellular heterogeneity and gene regulation.

Purpose of the Study:

To introduce SCOTCH (Single-Cell Omics for Transcriptome CHaracterization), a comprehensive bioinformatics pipeline for isoform characterization from lr-scRNA-Seq data.
To provide a platform-independent solution supporting diverse sequencing technologies and protocols.

Main Methods:

SCOTCH models isoforms using non-overlapping sub-exons and dynamic thresholding for robust assignment.
It integrates read coverage with existing annotations and uses iterative clustering to reconstruct novel transcripts.
Poly(A)-aware filtering is employed to minimize false-positive structures.

Main Results:

Extensive simulations show improved quantification of known isoforms and enhanced reconstruction of novel isoforms compared to existing methods.
Analyses of human blood and cerebral organoid datasets confirm SCOTCH's ability to resolve cell-type-specific transcriptome profiles.
SCOTCH successfully uncovers experimentally supported novel isoforms.

Conclusions:

SCOTCH is an effective end-to-end pipeline for isoform characterization from lr-scRNA-Seq data.
It outperforms existing splice-graph-based methods in recovering true novel isoforms.
The pipeline enables deeper insights into cell-type-specific transcriptomes and facilitates the discovery of novel isoforms across multiple platforms.