Methylation Project (JCU)
- 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
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
Samtools
Bedtools
Minimap2
Bowtie2
- sudo apt-get update
- sudo apt-get install bowtie2
R
- sudo apt-get update
- sudo apt-get install r-base
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)
Lates Calcarifer reference genome http://laszlo.tll.org.sg/asb_genome/
- 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
- 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