Processng cuffnorm output

Question

[bharata1803]

I have finished the tophat+cufflinks workflow for both end (cuffdiff and cuffnorm, I use the latest version) like in this webpage: http://cole-trapnell-lab.github.io/cufflinks/manual/

So, I wonder is there any document/tutoriaal that shows how to process the output of cuffnorm? I know that the output is not compatible with DESeq library in R. So, any suggestion please or I need to reprocess the BAM/SAM file with ht-seq so that I can process with DESeq? Thank you.

[GouthamAtla]

What is the goal of your analysis ?

[bharata1803]

Thank you.

My goal is I want to check for a specific gene, the up/down regulation compare to normal reference. I hope I can get the result in some percentage change, for example, 50% expression value compare to normal or 150% expression value compare to normal, like that.

Answer 1

[GouthamAtla]

Running cuffdiff will give the Fold Change and p-values for each gene across two conditions. This should help you find out wether the gene of your interest is differentially expressed.

[bharata1803]

Thank you,

Currently, I'm trying to process the data from cuffdiff. But, I'm confused because the result of gene_id from cuffdiff mapped to many genes in the gene_exp.diff file. I only want to check one (or two with splicing variation) so, is there any mistake so that I get this result?