RT Journal Article
SR Electronic
T1 Sharq, A versatile preprocessing and QC pipeline for Single Cell RNA-seq
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 250811
DO 10.1101/250811
A1 Tito Candelli
A1 Philip Lijnzaad
A1 Mauro J Muraro
A1 Hindrik Kerstens
A1 Patrick Kemmeren
A1 Alexander van Oudenaarden
A1 Thanasis Margaritis
A1 Frank Holstege
YR 2018
UL http://biorxiv.org/content/early/2018/02/07/250811.abstract
AB Despite the meteoric rise of single cell RNA-seq, only a few preprocessing pipelines exist that are able to perform all steps from the original fastq files to a gene expression table ready for further analysis. Here we present Sharq, a versatile preprocessing pipeline designed to work with plate-based 3’-end protocols that include Unique Molecular Identifiers (UMIs). Sharq performs stringent step-wise trimming of reads, assigns them to features according to a flexible hierarchical model, and uses the barcode and UMI information to avoid amplification biases and produce gene expression tables. Additionally, Sharq provides an extensive plate diagnostics report for quality control and troubleshooting, including that of spatial artefacts. The diagnostics report includes measures of the quality of the individual plate wells as well as a robust assessment which of them contain material from live cells. Collectively, the innovative approaches presented here provide a valuable tool for processing and quality control of single cell RNA-seq data.