demultiplexing-stats

Demultiplexing stats report designed for NextSeq output.

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

Usage

Clone this repository:

git clone https://github.com/NYU-Molecular-Pathology/demultiplexing-stats.git

Change to the repo directory:

cd demultiplexing-stats/

Run the run.sh script:

./run.sh /path/to/demultiplexing_output_dir

• Example command:

./run.sh /production/170526_NB501073_0011_AHCJTYBGX2/Data/Intensities/BaseCalls/Unaligned/

Example Output

A full demonstration of the report template usage can be found in the demo branch here; you can try it by running the following commands:

• Clone this repo if you haven't already, and switch to the demo branch

git clone https://github.com/NYU-Molecular-Pathology/demultiplexing-stats.git
cd demultiplexing-stats
git checkout demo

• Demo data is in the test directory. Compile the script with it:

./run.sh test/ SampleReport

• Report output can be found in the SampleReport_demultiplexing_report.html file, and can be previewed here or here

Software

• R (tested on version 3.3)
  • ggplot2
  • XML
  • plyr
  • knitr
• pandoc version 1.13+
• bash (test on version 4.1.2)