Review papers on the topic of RNA-seq
General Guides
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Computational methods for transcriptome annotation and quantification using RNA-seq (May 2011) in Nature Methods
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From RNA-seq reads to differential expression results (Dec 2010) in Genome Biology
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RNA-Seq: a revolutionary tool for transcriptomics (2009) in Nature Reviews Genetics
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RNA sequencing: advances, challenges and opportunities (2011) in Nature Reviews Genetics.
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RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing (2012) in Nature Methods
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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
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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.
Update 2016;
http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8