As a learning experience I am playing around with RNA Seq fastQ data. My goal is to simply obtain matrix of gene expression values for each sample that I say go forward and cluster.
I am looking for recommendations on a workflow to use to achieve this.
I have never done this before, but based on my limited understanding, I am thinking I need to do the following:
Pre-process using fastqc, and aligning using tophat, and then use cufflinks to obtain expression values.
One main concern I have is running FASTqc on multiple samples/files at the same time. Is this possible?
Like I said, I am really new at this and trying familiarize myself, so any guidance/feedback is greatly appreciated.