Completely new to RNA sequencing and bioinformatics and I have been trying to figure things out on my own so far...I am trying to analyze my RNA-seq data and I have made it as far as using cufflinks on all my files to quantify my transcripts. So now I have a bunch of transcripts.gtf files for each of my samples. I think I am supposed to use cuffmerge but I don't know which .gtfs to merge. Say I wanted to compare differential expression of my two controls (two different untreated cells types). Do I merge the .gtf files produced by cufflinks for these two samples then use that merged.gtf file for cuffdiff? Honestly, I'm lost and I'm having a hard time understanding why I wouldn't just compare the accepted_hits.bam files from tophat to a reference genome .gtf without using cufflinks. Also, why would cuffcompare be used? I am so new to this, the explanations on the cufflinks website are going over my head.
Any help greatly appreciated.