I am very new to RNA-seq analysis and am trying to figure out my next steps. I ran Tophat, followed by Cufflinks, Cuffmerge, and CuffDiff. Now I am trying to figure out what software is best to continue my analysis and what my next steps should be.
I want to do clustering based on gene expression first. Should I use the fpkm_gene_tracking output file from CuffDiff for this? Do I need to normalize the data? Log transform it? At what point should I filter out genes with an fpkm<1? And what software is best to use? Should I use the CummeRbund package in R?
Does anyone know of any good tutorials for me to get a better grasp?
Thank you Thank you.