Off topic:Gene count table from STRINGTIE/BALLGOWN for WGCNA

Question

[devikaparvathy]

I am using Bowtie+Stringtie+Ballgown for differential expression analysis of certain microbial RNA-seq data. I also want to create a whole genome regulatory networks using WGCNA package. Is it possible to obtain NORMALIZED COUNT table from Stringtie/Ballgown to use in WGCNA? (I have previously used Cuffnorm outputs for WGCNA). My data has 10 samples each as control and non-control.