Review papers on RNA-seq (Biostars)

Informatics for RNA-seq: A web resource for analysis on the cloud

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

RNA-seq Analysis

RNAseq analysis notes from Ming Tang

List of RNA-seq Bioinformatics Tools

Extensive list on Wikipedia of RNA-seq bioinformatics tools needed in analysis, ranging from all parts of an analysis pipeline from quality control, alignment, splice analysis, and visualizations

A survey of best practices for RNA-seq data analysis

Gives awesome roadmap for RNA-seq computational analyses, including challenges/obstacles and things to look out for, but also how you might integrate RNA-seq data with other data types