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