Align RNA-seq with Tophat http://genomespot.blogspot.com/2012/12/align-rna-seq-reads-to-genome-with.html?m=1
generate RNA-seq count matrix http://genomespot.blogspot.com/2013/06/generate-rna-seq-count-matrix-part-1.html?m=1
count over exons http://genomespot.blogspot.com/2013/06/generate-rna-seq-count-matrix-part-2.html?m=1
Align like a boss http://genomespot.blogspot.com/2013/07/align-next-gen-sequencing-data-like-boss.html?m=1
I will need to follow the RNA-seq nature protocol here Two nature protocols for RNA-seq analysis
Too much need to learn :) I found blogs are very good places to learn new stuff. That's also one of the reasons why I am writing this blog.