Plot normalized counts for a gene


Given a table of read counts for an experiment, this tool makes a plot of the normalized counts using the DESeq2 Bioconductor package.



This tool takes as input a table of raw counts. The count table has to be associated with a phenodata file describing the experimental groups. These files are best created by the tool "Utilities / Define NGS experiment", which combines count files for different samples to one table, and creates a phenodata file for it.

The tool normalizes counts by sequencing depth and adds a pseudocount of 1/2 to allow for log scale plotting. The counts are grouped by "group".


The plot of normalized counts.


This tool uses the DESeq2 package. Please read the following article for more detailed information:

M Love, W Huber and S Anders: Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol. 2014 15:550