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.

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.

• NOTE: This guide was designed using the latest HiC-Bench version at commit id f3d7a306aebaa5a3dfbcdcebc83a4ccedc513ccd. If newer version have changed compatibility with this demo, you can go back to that version of HiC-Bench by running:

cd hic-bench
git checkout f3d7a306aebaa5a3dfbcdcebc83a4ccedc513ccd

before proceeding with the rest of the demo.

This Demo

Clone this demo repository, and change to its directory

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

Usage

From within this directory, make a new directory for the analysis, and start a new HiC-Bench analysis there:

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

Change to that directory:

cd sample-project

and finish pipeline setup;

• 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 400

• 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.

• run the pipeline

# need to be in the parent analysis dir
cd ..
code.main/pipeline-execute sample-project [email protected]