## Plot normalized counts for a gene

### Description

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

### Parameters

- Gene name
- Show names in plot (yes, no) [no]

### Details

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".

### Output

The plot of normalized counts.

###
References

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