This code is associated with the paper from Wells et al., "ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair". eLife, 2020. http://doi.org/10.7554/eLife.53392
Zcwpw1 is co-expressed with Prdm9 and has domains that bind to both H3K4me3 and H3K36me3 (which are desposited by Prdm9 and required for its role in recombination.)
Software dependencies are managed as a Conda environment detailed in setup.sh
Details of the original FASTQ files, and ID-to-description mappings are included in Sample_Manifest.Rmd
To find the code for a specific figure see the Figure_Manifest.Rmd
The directory containing fastq files for each group and the genome specification is contained in the file config.yml
Most of the analyses are arranged as snakemake pipelines for reproducibility:
# Map reads to genome etc.
# Add FASTQ dir path & genome type to config.yml first
snakemake --snakefile pipelines/Map_Reads.py -npr --dag --forceall --config GROUP="Dmc1_r1" | dot -Tpdf > Map_Reads_dag.pdf
snakemake --cores 15 --snakefile pipelines/Map_Reads.py -npr --config GROUP="659233"
snakemake --cores 15 --snakefile pipelines/Map_Reads.py -npr --config GROUP="538916"
snakemake --cores 15 --snakefile pipelines/Map_Reads.py -npr --config GROUP="594404"
snakemake --cores 15 --snakefile pipelines/Map_Reads.py -npr --config GROUP="NA15"
snakemake --cores 15 --snakefile pipelines/Map_Reads.py -npr --config GROUP="Dmc1_r1"
snakemake --cores 13 --snakefile pipelines/Map_Reads.py -npr --config GROUP="733693"
# Call Peaks
snakemake --cores 15 --snakefile pipelines/Call_Peaks.py -npr
# make enrichment profile plots (& center/strand by motif if possible)
snakemake --cores 15 --snakefile pipelines/Plot_Profile2.py -npr
snakemake --cores 15 --snakefile pipelines/Plot_Heatmap.py -npr
# force-call
# specify sample pairs to force call in sample_pairings.py
# specify locations to call at in config.yml
snakemake --cores 15 --snakefile pipelines/Force_Call_Peaks.py -npr
snakemake --cores 15 --snakefile pipelines/wgs.py -npr
# Perform analysis of DMC1 data
cd dmc1
snakemake --cores 15 --snakefile pipelines/dmc1.py -npr
# plot profile over gene
metagene_plot.sh
snakemake --cores 10 --snakefile pipelines/analyse_peaks.py -npr
snakemake --cores 3 --snakefile pipelines/non_chip_analysis.py -npr
Other analyses are Rnotebooks, and require the preprocess.sh script to be run to generate the required files.