RNA-seq step by step demonstration

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 http://crazyhottommy.blogspot.com/2013/08/two-nature-protocols-for-rna-seq.html

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.