Question: How do you extract raw counts from CUFFLINKS?
2
gravatar for gtho123
4.7 years ago by
gtho123210
New Zealand
gtho123210 wrote:

I would like to extract the raw counts from my RNA-Seq experiment from Cufflinks. I know the arguments about alternate splicing but I am trying to compare different differential expression methods in my model plant. 

While the Cufflinks manual is very clear. In the Cuffnorm section it says these reads "should not be used with downstream differential expression tools that require raw counts as input.

However, the CummRbund release schedule says that "raw and normalized count tables and associated statistics all features" have been available for some time. From what I can tell this is the obtained from the count() function. However in the example the count column values seem normalised. So I would like to check are these values appropriate to use in applications like DESeq and edgeR? 

If not is there another way to get these values?

rna-seq • 3.2k views
ADD COMMENTlink modified 7 months ago by magdalena123610 • written 4.7 years ago by gtho123210
3
gravatar for Devon Ryan
4.7 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

Just use htseq-count or featureCounts. If some random value column from cufflinks agrees with these values then you'll know for the future which one to use. Cufflinks is a complicated enough program that one needs to go through the code to actually know what's truly going on, so I would strongly dissuade you from using any of it's values in DESeq2/edgeR/etc. without checking in a couple samples if they match what's expected.

ADD COMMENTlink written 4.7 years ago by Devon Ryan89k
0
gravatar for magdalena1236
7 months ago by
magdalena123610 wrote:

Just multiply each samples count table by the library size factors, Trapnell's answer here: https://github.com/cole-trapnell-lab/cufflinks/issues/12

ADD COMMENTlink written 7 months ago by magdalena123610
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