Close
Help




JOURNAL

Bioinformatics and Biology Insights

A Computational Pipeline for Cross-Species Analysis of RNA-seq Data Using R and Bioconductor

Submit a Paper


Bioinformatics and Biology Insights 2015:9 165-174

Original Research

Published on 02 Dec 2015

DOI: 10.4137/BBI.S30884


Further metadata provided in PDF



Sign up for email alerts to receive notifications of new articles published in Bioinformatics and Biology Insights

Abstract

RNA sequencing (RNA-seq) has revolutionized transcriptome analysis through profiling the expression of thousands of genes at the same time. Systematic analysis of orthologous transcripts across species is critical for understanding the evolution of gene expression and uncovering important information in animal models of human diseases. Several computational methods have been published for analyzing gene expression between species, but they often lack crucial details and therefore cannot serve as a practical guide. Here, we present the first step-by-step protocol for cross-species RNA-seq analysis with a concise workflow that is largely based on the free open-source R language and Bioconductor packages. This protocol covers the entire process from short-read mapping, gene expression quantification, differential expression analysis to pathway enrichment. Many useful utilities for data visualization are included. This complete and easy-to-follow protocol provides hands-on guidance for users who are new to cross-species gene expression analysis.



Downloads

PDF  (484.53 KB PDF FORMAT)

RIS citation   (ENDNOTE, REFERENCE MANAGER, PROCITE, REFWORKS)

Supplementary Files 1   (43.01 KB DOC FORMAT)

BibTex citation   (BIBDESK, LATEX)

XML




Quick Links


New article and journal news notification services