I am using both DESeq2 and Cufflinks2 for differential expression analysis for some mouse RNAseq data. I was reading this guide (http://chagall.med.cornell.edu/RNASEQcourse/Intro2RNAseq.pdf) for help. Page 49 of the guide says that RPKM/FPKM isn't suitable for differential expression analysis, since it doesn't take into account sequencing depth among different samples. However, I figured that going from Cufflinks to Cufflinks2, the developers would have accounted for this issue. Can I trust my results from Cufflink2? I am making a poster right now, and I don't want to put my Cufflinks2 results if they're not reliable