mev-normalize

This repository contains a WebMeV-compatible tool for RNA-seq normalization. We provide a number of commonly used transformations.

The result is a normalized count matrix.

---

To run external of WebMeV:

Either:

• build the Docker image using the contents of the docker/ folder (e.g. docker build -t myuser/normalize:v1 .)
• pull the docker image from the GitHub container repository (see https://github.com/web-mev/mev-normalize/pkgs/container/mev-normalize)

To run, execute the following:

docker run -d -v $PWD:/work <IMAGE> /usr/local/bin/run.sh /work/<path to raw counts in TSV format> <normalization method> <perform log transform on result?>

(here, we mount the current directory to /work inside the container- we assume your current working directory has the raw count matrix you are attempting to normalize)

The <normalization method> is one of those included in operation_spec.json:

• "CSS" (cumulative sum scaling. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010126/)
• "TSS" (total sum scaling)
• "DESeq2" (by DEseq2's median-based method)
• "TMM" (by edgeR's trimmed means of M value)
• "UQ" (upper quartile)

The final argument dicates whether to log-transform the resulting normalized counts. Use 0 (no) or 1 (yes).

This will create an output file (the normalized counts in TSV format) in your current directory.