Question: Cuffcompare or Cuffmerge for tissue specificity?
gravatar for colin.kern
4.9 years ago by
United States
colin.kern920 wrote:

I have RNA-seq libraries from 8 tissues (2 biological replicates for each). I want to determine which transcripts have tissue-specific expression. After I build cufflinks annotations for each of the individual tissues, would it be better to combine them into a single annotation using cuffmerge or cuffcompare? I'm concerned that if only one of the tissues has an assembled transcript at a specific loci, cuffmerge may consider it to not have enough evidence to include. But that's exactly the type of thing I'm interested in finding. Am I misunderstanding how cuffmerge works? It seems like cuffcompare might be better in this situation as it just does a straightforward union of all fragments.

rna-seq cufflinks • 1.1k views
ADD COMMENTlink modified 4.9 years ago by vivekbhr620 • written 4.9 years ago by colin.kern920
gravatar for vivekbhr
4.9 years ago by
vivekbhr620 wrote:

You can safely use cuffmerge for merging. It causes no loss of detected transcripts.

Also you will find this post useful..

ADD COMMENTlink modified 10 months ago by RamRS30k • written 4.9 years ago by vivekbhr620

Thanks for the answer. I tried both and I get 33886 XLOCs with cuffmerge and 51144 with cuffcmp. Also almost twice the number of TCONS. It says in the cuffmerge manual that it "automatically filters a number of transfrags that are probably artfifacts." Could this be what's causing the difference?

ADD REPLYlink written 4.9 years ago by colin.kern920

Did you use the reference annotation (ensembl gtf) with cuffcompare?

ADD REPLYlink written 4.8 years ago by vivekbhr620
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