Demo HiC-Bench ChIP-Seq Pipeline

designed for use in NYU Langone Medical Center

This demo will walk you through the setup for a ChIP-Seq analysis. See more docs for this pipeline here.

Installation

HiC-Bench

Make sure you've got HiC-Bench installed. This is typically installed in your home directory.

cd
git clone https://github.com/NYU-BFX/hic-bench.git

If you're working on the phoenix server at NYU, make sure you have your data directory linked to Aris's. This contains the reference data needed for the pipeline.

cd hic-bench
ln -s /ifs/home/at570/disk1/Resources/Code/pipeline-master/data data

NOTE: you might have to delete the broken data symlink before you can reset it.

Compile binaries.

cd code/src
make

This should produce various gtools* and tools* binaries in code/bin.

This Demo

Clone this demo repository, and change to its directory

git clone https://github.com/NYU-BFX/hic-bench-demo.git
cd hic-bench-demo

Usage

From within this directory, create a new project (which creates a new directory) for the analysis.

~/hic-bench/code/code.main/pipeline-new-analysis chipseq-standard sample-project

Change to the project directory.

cd sample-project

Set input files.

./code/setup-sample-files.sh ../source_data/

Create sample sheet template from samples, supplying genome version and fragment size.

cd inputs/
./code/create-sample-sheet.tcsh hg19 200

Manually open the inputs/sample-sheet.tsv file (e.g. in Excel, etc.) and match up the Input samples with the experimental samples. Refer to the samplesheet provided with this repository for an example of what it should look like.

Clean up the sample sheet.

mac2unix sample-sheet.tsv
sed -i 's/"//g' sample-sheet.tsv

Run the pipeline.

# need to be in the parent analysis dir
cd ..
code.main/pipeline-execute sample-project yourname@nyumc.org

Monitor progress.

watch qstat