Do you work with RNA-Seq data?
Do you plan to work with RNA-Seq data?
Have you ever heard of RNA-Seq data?

If the answer to any of these questions is 'yes' (or even 'maybe') then you should definitely check out this fantastic online guide to all things RNA-Seq:

RNA-seqlopedia

The RNA-seqlopedia provides an overview of RNA-seq and of the choices necessary to carry out a successful RNA-seq experiment

Written by Rodger Voelker and Clay Small of the Cresko Lab at the University of Oregon, it is a fantastically detailed, beautifully written resource to walk you through every step of working with RNA-Seq data.

I wish there were more online guides like this! Here's the Table of Contents, with the 'Analysis' section expanded, to give you a feeling for what it covers:

Experimental Design

RNA Preparation

Library Preparation

Sequencing

Analysis
Overview

Initial Processing

Demultiplexing

Removing adapters

Trimming

Kmer Normalization

de Novo Assembly

de Bruijn Graph assembly

Overlap Layout Assembly

Aligning reads to a reference

Aligning to a ref. genome

Aligning to a transcriptome

microRNA Aligners

Short Read Aligners Output

Annotation of transcripts

Differential gene expression

Normalization

Discrete Discrete Models

Continuous Discrete Models

Nonparametric Models

Choice of Analysis Software

References