Hello everyone,
I have 54 HT-seq Count files from an old experiment that I am reanalyzing. They are composed of combinations of the 2 treatment groups (Wildtype and Treatment), 3 exposures (water, tBOOH, diquat), and 3 times points. I need to create a matrix of the normalized count data for each gene in each sample. I am not sure how to start, any help would be appreciated.
Thanks,
•
written
by
Krish Srinivasan •
2 answers
What you are looking for is extraction of counts after variance stabilizing transformation (vsd/vst) or rlog normalization. You can find both described clearly in the DESeq2 manual (2.1.2 Extracting transformed values).
Hi, this is pretty simple using DESeq2's counts function and has been asked many times before. See here and here for examples.
Log in to answer this question.
-
multiple condition and time course in RNA-seq
written by tiancaigg •
-
DESeq2 multiple conditions, time points and sample types
written by DHARMESH •
-
Analyzing time-series RNA-seq data using DEseq2
written by Rahul •
-
Best approach to analyze multiple groups in RNAseq experiment
written by Daniel •
-
RNA-seq analysis with 8 groups, 2 exposures and 2 batches, 1 group as control?
written by johnbarrow641 •
-
How to average normalized counts of biological replicates
written by marina.rot •
-
DESeq multiple factor question
written by jdhindsa1999 •
-
Strategies for merging RNAseq datasets
written by Nico80 •
-
HT-seq Counts Stranded option
written by Krish Srinivasan •
-
Setup for multiple strains, multiple conditions, and replicates
written by montezuma •
