RNA-Seq Workflow: Gene-level Exploratory Analysis and Differential Expression

Overview

Journal F1000Res

Specialties Biomedical Engineering
Science

Date 2015 Dec 18

PMID 26674615

Citations 207

Authors

Michael I Love

Simon Anders

Vladislav Kim

Wolfgang Huber

Affiliations

Soon will be listed here.

Abstract

Here we walk through an end-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results.

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