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.
There's a python script called prepDE.py in the Stringtie manual, which gives you raw count tables from your stringtie output. Maybe that´s what you need. Check the manual to see how to run it.
Bowtie is not a splice aware aligner - You should be using a splice aware aligner such as HISAT2, or STAR, otherwise your results will be wrong. I'd strongly suggest you use featurecounts + DESeq2, or kallisto/Salmon + tximport + DESeq2 to get normalised counts.