Everything you ever wanted to know about working with RNA-Seq data but were afraid to ask
- 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