Methylation_JCU

Methylation Project (JCU)

Requirement

Java >= v1.8.0_74
FastQC >= v0.11.9
Bismark >= v.022.3
Samtools >= v1.5
Bedtools >= v2.17.0
Minimap2 >= v2.17
Bowtie2 >= v2.2.3
Github >= v2.20.2
R >= v3.0

Install tools in linux (Ubuntu) environment

Github

sudo apt-get install git-core git-gui git-doc

Java

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install openjdk-7-jre
sudo apt-get install openjdk-7-jdk

FastQC

sudo apt-get update
sudo apt-get install fastqc

Bismark

see https://github.com/FelixKrueger/Bismark/tree/master/Docs

Samtools

see http://www.htslib.org/download/

Bedtools

see https://bedtools.readthedocs.io/en/latest/content/installation.html

Minimap2

see https://github.com/lh3/minimap2

Bowtie2

sudo apt-get update
sudo apt-get install bowtie2

sudo apt-get update
sudo apt-get install r-base

User's Guide

This github repository contains bash scripts for methylation study. User can run the scripts in a sequential number based on the numbering of each script filename. Example:

01_fastqc.sh ## Quality Control on raw reads using FastQC tool
02_trim_galore.sh ## remove low quality reads and trimming low quality bases from input reads using trim_galore tool
03_bismark_mapping.sh ## Mapping clean reads against reference genome using bismark tool
04_align_sex_gene.sh ## align genes of interest to reference genome to obtain the alignment position
05_subset_methyl_300up_200down.sh ## subset BAM files from step 3 (e.g. 03_bismark_mapping.sh)
06_bismark_mapping_subset_300up-200down.sh## rerun bismark on the subset BAM files from step 5 (e.g 05_subset_methyl_300up_200down.sh)

Reference

Lates Calcarifer reference genome http://laszlo.tll.org.sg/asb_genome/

Data in data folder

data/fish_sex_genes_TSS_300up_200down.bed # 300bp upstream and 200bp down of TSS of each gene
subsetTSSsequence.sh # Script to obtain sequences (FASTA) located around TSS area if needed

Download scripts

mkdir pipeline # create a new folder in a local machine
cd pipeline # change directory
git clone https://github.com/QFAB-Bioinformatics/Methylation_JCU # download this repo to local machine