sns-wes-downstream-analysis

Downstream analysis of SNS WES pipeline output.

Example Output

[[ A full HTML version of the report output can be previewed here or here. ]]

Usage

• First, run the SNS WES pipeline: https://github.com/igordot/sns

• Run the sns-wes-coverage-analysis pipeline on the results

• Enter the directory you ran the SNS pipeline in

cd <sns-output-dir>

• Clone this repository and enter the directory

git clone --recursive https://github.com/NYU-Molecular-Pathology/sns-wes-downstream-analysis.git
cd sns-wes-downstream-analysis

• Run

run.sh "<project_ID>" "<results_dirname>"

Example:

run.sh "NS17-03" "RUN_4"

Software Requirements

• pandoc version 1.13+
• R version 3.3.0, with the following packages:
  • ChIPpeakAnno
  • biomaRt