Question: Cuffmerge on all samples or only on those that I need to include in differential expression analysis?
gravatar for Sumit Paliwal
17 months ago by
Sumit Paliwal20 wrote:

Hi, I have performed RNA-seq on samples from two different conditions (each with atleast two or three replicates). I have aligned the samples using tophat and now wish to perform differential expression analysis using Cufflinks. I have a query about cuffmerge. I suspect a replicate sample from one condition to be an outlier. So, should I include this sample to generate the merged assembly file using cuffmerge or exclude it. What is the likely effect of this on differential expression analysis if I include/exclude it?

rna-seq cuffmerge cufflinks • 530 views
ADD COMMENTlink modified 17 months ago by Kevin Blighe37k • written 17 months ago by Sumit Paliwal20
gravatar for Kevin Blighe
17 months ago by
Kevin Blighe37k
Republic of Ireland
Kevin Blighe37k wrote:

Hi Sumit,

It depends on which basis you believe it to be an outlier? If it just has unusually high expression over the same transcripts that the other samples have, then including it should not be much of a problem for cuffmerge. However, if you believe that it shows expression in regions that it shouldn't (like, expression 'noise'), then cuffmerge will interpret these as genuine transcripts and will include them in the consensus transcriptome.


ADD COMMENTlink written 17 months ago by Kevin Blighe37k
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