Question: RNA-seq Analysis after CuffDiff: Clustering, etc
gravatar for Biology001
4.4 years ago by
United States
Biology0010 wrote:

Hello - 

I am very new to RNA-seq analysis and am trying to figure out my next steps. I ran Tophat, followed by Cufflinks, Cuffmerge, and CuffDiff. Now I am trying to figure out what software is best to continue my analysis and what my next steps should be.

I want to do clustering based on gene expression first. Should I use the fpkm_gene_tracking output file from CuffDiff for this? Do I need to normalize the data? Log transform it? At what point should I filter out genes with an fpkm<1? And what software is best to use? Should I use the CummeRbund package in R? 

Does anyone know of any good tutorials for me to get a better grasp? 

Thank you Thank you.

rna-seq clustering cuffdiff • 2.5k views
ADD COMMENTlink modified 4.3 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by Biology0010
gravatar for Jennifer Hillman Jackson
4.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


CummeRbund would be a great place to start. Several of the RNA-seq tutorials and training courses shared by the community here explain how to proceed:

Apologies for the delayed reply - your question was unfortunately missed earlier (my fault). Next time, I'll make certain you're first!

Best, Jen, Galaxy team

ADD COMMENTlink written 4.3 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour