Question: Cuffdiff showing 5k significat genes
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gravatar for Light
19 months ago by
Light20
Light20 wrote:

Helloeverybody, I have taken 2 per condition of RNA-seq for finding DEG and followed tuxedo workflow and after cuffdiff output am getting more than 5k significant genes? is it correct, cause i think its too much of gene list. Am in right path or not? PLease provide some comments.

ADD COMMENTlink modified 19 months ago by igor6.6k • written 19 months ago by Light20
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gravatar for mastal511
19 months ago by
mastal5112.0k
mastal5112.0k wrote:

It depends on how many genes your organism has, and what condition you are studying, are you studying something like a developmental stage where you would expect many of the genes to be changing their expression level?

ADD COMMENTlink written 19 months ago by mastal5112.0k

one sample from human infected with a virus and other one normal condition.

ADD REPLYlink written 19 months ago by Light20
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gravatar for igor
19 months ago by
igor6.6k
United States
igor6.6k wrote:

The number of significant genes can vary widely depending on many factors. Without knowing anything about your experiment, it's impossible for someone to say what is a reasonable amount. If you think you are getting too many genes, change the significance threshold. The cutoff is mostly arbitrary.

ADD COMMENTlink written 19 months ago by igor6.6k
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