Question: RNA-seq Analysis after CuffDiff: Clustering, etc
gravatar for Biology001
3.7 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 • 2.2k views
ADD COMMENTlink modified 3.6 years ago by Jennifer Hillman Jackson24k • written 3.7 years ago by Biology0010
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson24k 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 3.6 years ago by Jennifer Hillman Jackson24k
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