Question: Cuffmerge on all samples or only on those that I need to include in differential expression analysis?
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gravatar for Sumit Paliwal
22 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 • 654 views
ADD COMMENTlink modified 22 months ago by Kevin Blighe45k • written 22 months ago by Sumit Paliwal20
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gravatar for Kevin Blighe
22 months ago by
Kevin Blighe45k
Kevin Blighe45k 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.

Kevin

ADD COMMENTlink written 22 months ago by Kevin Blighe45k
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