This question is similar to this. I have RSEM output files namely "quatify.genes.result" and "quatify.isoform.result". My question is reagarding the downstream analysis, I want to get differential expressed genes. the quatify.genes.result file has two columns one expected counts and FPKM value. How to convert these expected counts to raw counts, so that I can use DESEQ or DEGseq. Could anyone suggest me other other softwares for the downstream analysis on RSEM output/ or what could be a better approach to this.