Question: Each sample as a condition? - cuffdiff
0
gravatar for ctoscano
2.9 years ago by
ctoscano0
United States
ctoscano0 wrote:

Hello everyone,

I've been having doubts about running each sample as a condition to get the FPKM trancking file as a table with all of the results and not the condesed one for each condition. Is is possible? Can it generate errors?

Thanks.

cufflinks galaxy • 906 views
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by ctoscano0
3
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

You want to compare two samples from the same condition as individual conditions? Cuffdiff does not inherently know where the data is from so I wouldn't expect true errors.

This could be used as a test of sorts, a way of understanding more about the contents of each sample. Just be aware that this is a test and the differential expression results will be none to very small between two samples from the same condition for a reasonably "good" dataset. 

Best, Jen, Galaxy team

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson25k
0
gravatar for ctoscano
2.9 years ago by
ctoscano0
United States
ctoscano0 wrote:

Well I want to get a condensed FPKM table with each sample on it, thats why I want to run the samples separetaly. I'll run cuffdiff with each condition for the differential expressed genes too. 

ADD COMMENTlink written 2.9 years ago by ctoscano0
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