I'm new to this so bear with me. I've been using Galaxy to process raw RNA-Seq FASTQ data into FPKM matrices. My understanding is that you can't directly compare the cufflinks output of different samples, that rather you have to use some comparison algorithm to be able to appropriately compare.
I've gone directly from cufflinks to cuffdiff and that seems to give me a perfectly useable gene_FPKM tracking file. However, is that appropriate? Or do I need to use cuffnorm or cuffquant at some point?
I appreciate your help whoever has a spare minute!