Bioinformatics analysis of single-cell RNA-seq raw data from iPSC-derived neural stem cells

Jeffrey Kim, Marcel M. Daadi

Research output: Chapter in Book/Report/Conference proceedingChapter

8 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press
Pages145-159
Number of pages15
DOIs
StatePublished - 2019

Publication series

NameMethods in Molecular Biology
Volume1919
ISSN (Print)1064-3745

Keywords

  • BBDuk
  • Bioinformatics
  • C1
  • DAVID
  • FASTQC
  • Fluidigm
  • Kallisto
  • Neural stem cells
  • RNA-seq
  • SCDE
  • Single cell
  • Single-cell analysis
  • Single-cell RNA-seq
  • Singular
  • Sleuth

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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