Isoform-level quantification for single-cell RNA sequencing.

ABSTRACT:

Motivation

RNA expression at isoform level is biologically more informative than at gene level and can potentially reveal cellular subsets and corresponding biomarkers that are not visible at gene level. However, due to the strong 3' bias sequencing protocol, mRNA quantification for high-throughput single-cell RNA sequencing such as Chromium Single Cell 3' 10× Genomics is currently performed at the gene level.

Results

We have developed an isoform-level quantification method for high-throughput single-cell RNA sequencing by exploiting the concepts of transcription clusters and isoform paralogs. The method, called Scasa, compares well in simulations against competing approaches including Alevin, Cellranger, Kallisto, Salmon, Terminus and STARsolo at both isoform- and gene-leve

SUBMITTER: Pan L 

PROVIDER: S-EPMC8826380 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature