Usefull manuals for young bioinformatician

This page contains a lot of truly essential manuals and pipelines for bioinformatics analysis of biological data:

manuals.bioinformatics.ucr.edu

Handling of RNA-seq data

For everyone, who is working with RNA-seq data I would like to advise this comprehensive protocol, published in Nature. The protocol describes in details all steps of data analysis, as well as trouble shooting.

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor