Bioinformatics Analysis of Single-Cell RNA-Seq Raw Data from iPSC-Derived Neural Stem Cells

Abstract

This chapter describes a pipeline for basic bioinformatics analysis of single-cell sequencing data (see Chap. 10 : Single-Cell Library Preparation). Starting with raw sequencing data, we describe how to quality check samples, to create an index from a reference genome, to align the sequences to an index, and to quantify transcript abundances. The curated data sets will enable differential expression analysis, population analysis, and pathway analysis.

Keywords: BBDuk; Bioinformatics; C1; DAVID; FASTQC; Fluidigm; Kallisto; Neural stem cells; RNA-seq; SCDE; Single cell; Single-cell RNA-seq; Single-cell analysis; Singular; Sleuth.