Question: (Closed) Gene count table from STRINGTIE/BALLGOWN for WGCNA
1
gravatar for devikaparvathy
3.0 years ago by
India
devikaparvathy20 wrote:

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.

rna-seq ballgown stringtie wgcna • 4.9k views
ADD COMMENTlink modified 2.9 years ago by Albert140 • written 3.0 years ago by devikaparvathy20

Hello devikaparvathy!

We believe that this post does not fit the main topic of this site.

The issue was resolved.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

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ADD REPLYlink written 23 months ago by devikaparvathy20
5
gravatar for Albert
2.9 years ago by
Albert140
Dublin, Ireland
Albert140 wrote:

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

ADD COMMENTlink written 2.9 years ago by Albert140

really helpful. thanks very much.

ADD REPLYlink written 2.4 years ago by pilyric0

If this answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

ADD REPLYlink written 2.4 years ago by WouterDeCoster40k
1
gravatar for andrew.j.skelton73
2.9 years ago by
London
andrew.j.skelton735.8k wrote:

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.

ADD COMMENTlink written 2.9 years ago by andrew.j.skelton735.8k

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.

ADD REPLYlink written 23 months ago by devikaparvathy20
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