ChIP-seq-snakemake

Conda Enviornment

conda install -c bioconda -c conda-forge bowtie sra-tools samtools fastp bowtie2 bwa bowtie bedtools snakemake picard

GATK Download

wget  https://github.com/broadinstitute/gatk/releases/download/4.0.6.0/gatk-4.0.6.0.zip
unzip gatk-4.0.6.0.zip
cd /GATK/gatk-4.0.6.0
./gatk --help

Files needed for analysis

blacklist

wget http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg19-human/wgEncodeHg19ConsensusSignalArtifactRegions.bed.gz

How To Execute

File Tree (fastq files are saved in rawfastq file)

workspace

ChipSeq_snakemake.py
rawfastq

SRR539135_1.fastq.gz
SRR539135_2.fastq.gz
SRR13242842_1.fastq.gz
SRR13242842_2.fastq.gz

snakemake -s ChipSeq_snakemake.py -p -j 1 --config workspace=path-to-workspace \
genomes=path-to-bwa-index \
blacklist=path-to-blacklist-file \
GATK=path-to-gatk 

example

snakemake -s ChipSeq_snakemake.py -p -j 1 --config workspace=/mnt/d/lxq/Training/Chip-Seq \
genomes=/mnt/d/lxq/Training/WES/GATK/hg38/bwa_index \
blacklist=/mnt/d/lxq/Training/reference \
GATK=/mnt/d/lxq/Training/WES/GATK/gatk-4.1.7.0/gatk 

result

The pipeline generates 17 files for one sample, which call_peaks file is the result file needed for downstream analysis. File tree shown below: