Bioinformatics Core Facility
National Institute of Biotechnology in the Negev, Ben Gurion University.
This workflow automates a standard ChIP-seq analysis.
This workflow is based on a workflow kindly provided by Dr. Dena Leshkowitz of the Life Sciences Core Facilities, Weizmann Institute of Science.
The ChIP-seq workflow is in active development.
Preparation and QA: a. Merging the reads into a single file per sample (
merge). b. QC with fastqc (
fastqc_html) c. Trimming with trimmomatic (
trimmo) d. QC on trimmed reads with fastqc e. Adding the genome and the GTF file to the project (
Mapping a. Creating a bowtie2 index for the genome (
bowtie2_builder) a. Mapping the reads to the reference genome with bowtie2 (
bowtie2_mapper) b. Conversion to sorted BAM with samtools (
samtools) c. Sorting by name for bedGraphToBigWig with the
Genericmodule. c. Converting to UCSC and IGV format (
Finding ChIP peaks a. Peak calling is performed with macs2 callpeak (
macs2_callpeak) b. Further analysis of the peaks is done with macs2 bdgcmp (
In this workflow, we added the genome and GTF file via the parameter file. It is possible to add them via the sample file, as well.
fastq files, either paired-end or single-end.
A sample to control mapping (see Example sample lines below)
All programs can be installed with CODDA. See section Quick start with conda
Title ChIP_project #SampleID Type Path lane Sample1 Forward /path/to/Sample1_F1.fastq.gz 1 Sample1 Forward /path/to/Sample1_F2.fastq.gz 2 Sample1 Reverse /path/to/Sample1_R1.fastq.gz 1 Sample1 Reverse /path/to/Sample1_R2.fastq.gz 2 Sample2 Forward /path/to/Sample2_F1.fastq.gz 1 Sample2 Reverse /path/to/Sample2_R1.fastq.gz 1 Sample2 Forward /path/to/Sample2_F2.fastq.gz 2 Sample2 Reverse /path/to/Sample2_R2.fastq.gz 2 Sample_Control Sample1:Sample2
The workflow file is available
For easy setup of the workflow with CONDA, use the following instructions:
Create and activate a conda environment with all the required programs:
curl -LO https://raw.githubusercontent.com/bioinfo-core-BGU/neatseq-flow-modules/master/docs/source/Workflow_docs/ChIP_seq_conda.yaml conda env create -n ChIP_seq_WF -f ChIP_seq_conda.yaml source activate ChIP_seq_WF
Create a sample file. It should look like the file shown in Example of Sample File. Don’t forget to replace the sample names and file paths:
Make sure the file is TAB-delimited!
To get the full path to a file, use the following command:
readlink -f <filename>
Get the parameter file with:
curl -LO https://raw.githubusercontent.com/bioinfo-core-BGU/neatseq-flow-modules/master/Workflows/ChIP_seq.yaml
Run the workflow: