WGBS Pipeline

There are two forms of the pipeline:

1. Native app for Basespace

2. Localized app

Both Require the Installation of the following packages, however the initialization script will do this for you:

1. BWA-Meth: look to WGBS-Pipeline/nativeApp/Scripts for installtion

https://github.com/brentp/bwa-meth

2. Pile-O-Meth: look to WGBS-Pipeline/nativeApp/Scripts for installtion

https://github.com/dpryan79/PileOMeth

3. Bedtools: look to WGBS-Pipeline/nativeApp/Scripts for installtion

http://bedtools.readthedocs.org/en/latest/index.html

4. Metilene: look to WGBS-Pipeline/nativeApp/Scripts for installtion

http://www.bioinf.uni-leipzig.de/Software/metilene/

#WGBS/nativeApp/:

Instructions

1. Dockerfile

2. scripts/

a) Form_Builder.json

b) call_back.js

c) Dependencies/

bwa_meth.sh
pileometh.sh
bedtools.sh
metilene.sh

c) data/input/

AppSession.json

d) tmp/scripts/

Full_Pipeline.sh

3. Reference/

a) Human Chromosomes:

Chr 1-22
X, Y, M

b) Mouse Chromsomes:

Chr 1-19
X, Y, M

c) Human Genomes:

HG19, HG38 

d) Mouse Genomes:

mm9, mm10

c)

#WGBS/Local/

before beginning this process, place all of the raw fastq files to be analyzed into the data/input folder