Abstract
Summary: SCReadCounts is a method for a cell-level estimation of the sequencing read counts bearing a particular nucleotide at genomic positions of interest from barcoded scRNA-seq alignments. SCReadCounts generates an array of outputs, including cell-SNV matrices with the absolute variant-harboring read counts, as well as cell-SNV matrices with expressed Variant Allele Fraction (VAFRNA); we demonstrate its application to estimate cell level expression of somatic mutations and RNA-editing on cancer datasets. SCReadCounts is benchmarked against GATK and Samtools and is freely available as a 64-bit self-contained binary distribution (Linux), along with MacOS and Python installation.
Availability: https://github.com/HorvathLab/NGS/tree/master/SCReadCounts
Publisher
Cold Spring Harbor Laboratory
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