I am developing a pipeline from Simulated RNA-seq datasets. I want to benchmark Different quantification tools now.Some tools like HTSeq and Featurecounts are giving the gene abundance in counts, and some are like cufflinks, RSEM and eXpress giving in Normalized FPKM or TPM values. Now my question is How can I compare these all tools ? because they are giving results in a different way.
Should I convert both Counts (from HTSeq and FeatureCounts) and FPKM into TPM or some think ? Is this a good way? Thanks in advance.