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.
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devikaparvathy •
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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.
Manual: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual Script: https://ccb.jhu.edu/software/stringtie/dl/prepDE.py
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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.
Sorry i had somehow missed your comment, I was working on a prokaryotic dataset and hence used BowTie. I used cufflinks suit to obtaine the normalized gene count.
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