Need suggestions for RNA-seq quantification tools benchmarking.

Question

[k.kathirvel93]

Hi EveryOne,

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.

[ATpoint]

Is this a thesis project? I am asking because you (IMHO) will barely find any field in bioinformatics that is more saturated than RNA-seq quantification and its downstream analysis. There are plenty of tools and pipelines, all developed for different purposes, and with different pros and cons, for both gene - and transcript level quantification. What exactly is the goal of your study, because changes are high that a well-maintained and elaborate pipeline already exists for this?

[k.kathirvel93]

My aim is differential expression analysis

[ATpoint]

Your other post seems to go into the same direction, and I gave my opinion on what I would do in your case there.