Tutorial:Rna-Seq Review Papers

Question

[Istvan Albert]

Review papers on the topic of RNA-seq

General Guides

• Computational methods for transcriptome annotation and quantification using RNA-seq (May 2011) in Nature Methods
• From RNA-seq reads to differential expression results (Dec 2010) in Genome Biology
• RNA-Seq: a revolutionary tool for transcriptomics (2009) in Nature Reviews Genetics
• RNA sequencing: advances, challenges and opportunities (2011) in Nature Reviews Genetics.
• RNA-Seq - quantitative measurement of expression through massively parallel RNA-sequencing (2012) in Nature Methods
• The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis (2012) in Mol Ecol Resour see also the Simple Fools Online Guide

Tophat and Cufflinks

Tophat is a tool to align RNA-seq reads, Cufflinks assembles transcripts, and estimates their abundances

• Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks (March 2012) Nature Protocols

Transcriptome Assembly

• Next-generation transcriptome assembly (2011) in Nature Reviews Genetics

Biostar Tags

• rna-seq+rnaseq
• tophat+cufflinks+cuffdiff+cuffcompare

Back to the Table of Contents

[Malachi Griffith]

Here is a review/educational paper "Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud" that accompanies an extensive hands-on tutorial at rnaseq.wiki. It covers many aspects of RNA-seq and includes primers on related fundamentals that you will need including Unix, R, Genome Browsers, using cloud computing, etc.

[Medhat]

Update 2016;

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8

Answer 1

[NextGenSeek]

Here is more.

RNA-Seq: a revolutionary tool for transcriptomics. Zhong Wang, Mark Gerstein & Michael Snyder, Nature Reviews Genetics 10, 57-63 (January 2009)

Next-generation transcriptome assembly. Jeffrey A. Martin & Zhong Wang Nature Reviews Genetics 12, 671-682 (October 2011)

RNA sequencing: advances, challenges and opportunities Fatih Ozsolak & Patrice M. Milos, Nature Reviews Genetics 12, 87-98 (February 2011)

RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing Brian T. Wilhelma and Josette-Renée Landryb, Methods Volume 48, Issue 3, July 2009, Pages 249–257

[Istvan Albert]

I am going to add the checkmark to any post that is merged into the toplevel one

Answer 2

[NextGenSeek]

Models for transcript quantification from RNA-Seq, Lior Pachter, preprint arXiv 2012

Computation for ChIP-seq and RNA-seq studies. Pepke, Shirley; Wold, Barbara; Mortazavi, Ali, Nature methods. 2009 6(11 Suppl):S22-32

Answer 3

[upendrakumar.devisetty]

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA‐seq experiments

Molecular Ecology

Nagarjun Vijay Jelmer W. Poelstra Axel Künstner Jochen B. W. Wolf

RNA-Seq Assembly – Are We There Yet?

Simon Schliesky,1 Udo Gowik,2 Andreas P. M. Weber,1 and Andrea Bräutigam1,*