First my sincere thanks to all community members. Posts here really helps people like us who are new in the field.
Recently I completed a RNA-Seq project consisting 25 samples with 3 biological replicates each. In brief, due to absence of a reference genome for the organism of interest, I performed denovo transcriptome assembly followed by redundancy removal, estimating raw read counts, and differential expression using DeSeq2. Now I need to perform co-expression using WGCNA package, which I have done only once before but it was using output from tuxedo pipeline.
Now from DeSeq2, I have the normalized, rlog, variance stabilized counts, but the count matrix has 75 entries (25 samples x 3 replicates). Earlier in output from Tuxedo pipeline fpkm obtained were after collapsing the biological replicates. So seek help or any suggestion on how to handle the biological replicates for WGCNA analysis from DeSeq2 output (mention in previous lines) or can the biological replicates be collapsed somehow in order to perform co-expression on final set of 25 samples. Everywhere it is suggested not to use DeSeq2's collapseReplicates for biological replicates.
I have been searching for solution for sometime and really appreciate any help or suggestion to proceed further. Thanks.