moonerss / chip_seq_snakemake Goto Github PK

This is a simple utility to analyse CHIP-seq data with a selection of popular tools. It is written in snakemake that allows the user to scale it to any system. Currently, it contains analyses with the following tools:

• fastqc(quality control for reads)
• trim_galore(Adapter trimming)
• cutadapt(Adapter trimming)
• bowtie2(alignment)
• picard(Mark duplicates)
• deeptools(Generate gene-body meta-profile from bigWig files, Calculate genome-wide IP enrichment relative to control)
• phantompeakqualtools(Calculate strand cross-correlation peak and ChIP-seq quality measures including NSC and RSC)
• MACS2(Call broad/narrow peaks)
• HOMER(Annotate peaks relative to gene features)

For installation purposes, it is a good idea to make a new python virtual environment and install snakemake on it, and then download all the tool binaries in your desired location. Following this, retrieve the repository using git;

git clone https://github.com/Moonerss/chip_seq_snakemake.git

The only other modification that needs to be done is to edit the config/config.yaml and config/samplesheet_test.csv files to specify the location of files on your system, and then run following in the repository folder