I will be looking at four gonad and four brain tissue samples in female and male Loggerhead turtles. The raw data will have run through FastQC, Trimmomatic, and an RNA-Seq De novo assembly using Trinity.
I am hoping to look at the resulting transciptome reads for significant differences in genes that may be unique to either the tissue or gender of a Loggerhead turtle. In essence, I am looking for patterns across the following 2X2 table:
| Female | Male | |
| Brain | ||
| Gonad |
In other words,
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What are the significant genetic differences in brain and gonad tissues for female Loggerhead turtles?
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What are the significant genetic differences in brain and gonad tissues for male Loggerhead turtles?
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What are the significant genetic differences in brain tissues for female and male Loggerhead turtles?
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What are the significant genetic differences in gonad tissues for female and male Loggerhead turtles?
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Are there unique genes to the male Loggerhead brain tissue, female Loggerhead brain tissue, male Loggerhead gonad tissue, female Loggerhead gonad tissue?
With those research questions in mind, which WGCNA tutorial/s should I refer to for guidance? From what I understand, my first order of business is to create a gene network and detect modules. I am unsure how to use the output of transcriptome and converting it to an acceptable WGCNA input for matrices...can you explain how that would work? Thank you in advance!
