WGCNA from Salmon Output
I am working on RNA -seq data analysis, I have quantified my data using Salmon which has given me TPM values for all transcripts. Next, I want to perform Weighted gene coexpression analysis (WGCNA) using transcript TPM values. Is there a direct way to do this? or Do I have to preprocess the TPM values before going the WGCNA?
• 1,294 views
•
link
updated
by
jv
•
written
by
Adrij Pawan •
•
written
by
Adrij Pawan •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to obtain TPM data after batch effect correction from count data obtained using RSEM
written by Apprentice
-
WGCNA on TCGA case-control
written by Maliha •
-
TMM on a targeted RNA-Seq dataset
written by oakhamwolf •
-
How important is normalization for RNA_Seq data ?
written by sunnykevin97
-
salmon output to linear models in R
written by evelyn
-
RNA seq analysis using linear regression
written by evelyn
-
From transcript to gene - Salmon quantification
written by JulianC •
-
Data format for wcgna algorithm in R
written by ghataksoumyakanti •
-
Dealing with rRNA reads in differential expression analysis
written by msbio •
-
Have Salmon output tabular files from Galaxy; need to import into R for DESeq2
written by Dennis •
Why TPM? WGCNA is performed with log-transformed gene counts
I understand TPM values can not be directly used for WGCNA.However, i wish to know if we use TPM values with some additional processing steps?
Please see the following past posts regarding your question:
Is there a way where we can convert TPM to raw read count?
TPM to raw counts