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Calculating expression count values for WGCNA

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  • Calculating expression count values for WGCNA

    Hello all, I am trying to come up with a matrix of expression values for my samples to use in a weighted gene co-expression analysis (WGCNA), but am not sure what the best tool to use is. To date, the majority of my analysis has been done using the Galaxy platform. I have files with differential expression values between samples/treatments (using CuffDiff) but from my understanding, I cannot use these since they are biased(?)

    Should I: 1) begin my entire analysis from scratch on the command line so that I am consistent with treatment; 2) use Galaxy up until a certain point (after concatenating, quality-trimming, and removal of adapters from my fasq files), or 3) use Galaxy through the whole process until I have the data to feed into the WGCNA package ?

    Thank you for your time.