One is from Simon Anders, his group wrote the DESeq
http://www.nature.com/nprot/journal/v8/n9/full/nprot.2013.099.html
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
The other one
http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
I will go through a complete RNA-seq analysis following the guidelines.
There are other packages make RNA-seq analysis easier:
Blacktie https://pypi.python.org/pypi/blacktie/0.2.1
https://github.com/BradyLab/RNASeq
Nesoni http://www.vicbioinformatics.com/nesoni-cookbook/
Lots of things are waiting for me to try out!