Question: Need suggestions for RNA-seq quantification tools benchmarking.
0
gravatar for k.kathirvel93
2.2 years ago by
k.kathirvel93260
India
k.kathirvel93260 wrote:

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.

rna-seq next-gen • 718 views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by k.kathirvel93260

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?

ADD REPLYlink written 2.2 years ago by ATpoint38k

My aim is differential expression analysis

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by k.kathirvel93260

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

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by ATpoint38k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 570 users visited in the last hour