ChIP-seq.config.md

ChIP-seq configuration

Huitian Diao (Yolanda)

Oct 29, 2018

So easy, your grandfather could do this...

1. Bioconda

1.0 Install bioconda (If you never installed conda on your computer)

• Mac&Linux Miniconda Install instructions
• Windows Miniconda Install instructions (You can ignore the "Setup Spyder IDE" part)
• Mac&Linux&Windows Bioconda Install instructions (You can ignore the "dDocent" part)

1.1 Setting up python2.7 virtual environment

• Managing conda environment

conda create -n chip python=2.7
source activate chip # To activate the virtual environment

• All the following steps are under virtual environment chip. When virtual environment is activated, you can see (chip) at the start of your command prompt
• For using jupyter notebook in virtual environment, everything should be the same except before you type in jupyter notebook, use source activate chip

2. Tool installation

• 2.1 sra-tools
• 2.2 FastQC
• 2.3 MultiQC
• 2.4 Samtools
• 2.5 Trim-galore
• 2.6 Bowtie2
• 2.7 MACS2
• 2.8 USCS-bedgraphtobigwig
• 2.9 Rpy2

conda install sra-tools fastqc multiqc samtools trim-galore bowtie2 macs2 ucsc-bedgraphtobigwig
# Usage: trim_galore (can not call it by trim-galore :D)

3. R package installation

Option #1: Through Bioconda

ChIPQC and DEseq2

conda install -c bioconda bioconductor-chipqc bioconductor-deseq2

ChIPseeker and ClusterProfiler

conda install bioconductor-chipseeker bioconductor-clusterprofiler

Option #2: Through Bioconductor

If the installation through conda did not work for the bioconductor packages, please start a R kernel in jupyer notebook and then enter the following commands,

install.packages("BiocManager")
BiocManager::install(c("ChIPQC", "ChIPseeker", "clusterProfiler", "DESeq2"))