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