This ChIP-Seq analsysis pipeline (ChAP) will allow for step-by-step analysis of your paired-end ChIP-Seq NGS data. It can take either single-end or paired-end NGS data.
To download the repository (anywhere in /home):
git clone https://github.com/niekwit/ChIP-Seq-pipeline.git
All the dependencies are expected to be in the environment variables, except for Picard (this can be installed anywhere in /home).
- HISAT2 and bwa index files have to be build manually from fasta files. Their locations have to be changed in the
align.shfile (working on automatic detection). - Blacklisted regions can be found here, and their locations have to be changed in the
align.shfile (working on automatic detection).
Create a main folder with any name that contains the sub-folder raw-data. This sub-folder contains all the fastq.gz files. From the main folder run:
path/to/chip-seq-pipeline.sh [ fastqc ] [ align <aligner-pe/se> <species> ] [ dedup ] [ downsample ] [ qc ] [ bigwig ] [ peaks ] [ ngsplot ]
It is recommended that the analysis is performed in a step-wise manner. For example:
./chip-seq-pipeline.sh fastqc: check quality of fastq.gz files./chip-seq-pipeline.sh align bwa-pe human: align files to human genome (no deduplication performed)- One can use a genome browser to map the BAM files and decide whether deduplication is required
./chip-seq-pipeline.sh dedup: perform deduplication./chip-seq-pipeline.sh downsampling: perform downsampling on input file if read number is higher than corresponding ChIP sample./chip-seq-pipeline.sh qc: perform quality control of bam files and replicates./chip-seq-pipeline.sh bigwig: create BigWig files./chip-seq-pipeline.sh peaks: call/annotate peaks with MACS2/HOMER./chip-seq-pipeline.sh ngsplot: generate metagene plots and heatmaps