SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data.

ABSTRACT:

Background

Recent studies have demonstrated the utility of scRNA-seq SNVs to distinguish tumor from normal cells, characterize intra-tumoral heterogeneity, and define mutation-associated expression signatures. In addition to cancer studies, SNVs from single cells have been useful in studies of transcriptional burst kinetics, allelic expression, chromosome X inactivation, ploidy estimations, and haplotype inference.

Results

To aid these types of studies, we have developed a tool, SCReadCounts, for cell-level tabulation of the sequencing read counts bearing SNV reference and variant alleles from barcoded scRNA-seq alignments. Provided genomic loci and expected alleles, SCReadCounts generates cell-SNV matrices with the absolute variant- and reference-harboring read counts, as w

SUBMITTER: Prashant NM 

PROVIDER: S-EPMC8459565 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature