deeptools 25 repo

Setup

You need to have rust installed on your system before continuing, additionally, you need pixi and conda up and running too. Finally, your system needs internet access to download the required data.

Benchmark

Run the benchmark:

pixi run snakemake -s benchmark/benchmark.smk --cores 20 -d /path/to/working/directory --use-conda

Running specific functions only in the benchmark can be done by setting what in the config:

pixi run snakemake -s benchmark/benchmark.smk --cores 20 -d /path/to/working/directory --use-conda --config what=bamCoverage

What can take values 'alignmentSieve', 'bamCoverage', 'bamCompare', 'multibamSummary' or 'computeMatrix'. If any other value is provided (or none is set), all benchmarks will be ran. The os flag will be set automatically, but can also be provided manually (used in final benchmark table to keep track of platform benchmark was run on):

pixi run snakemake -s benchmark/benchmark.smk --cores 20 -d /path/to/working/directory --use-conda --config what=bamCoverage os=my_fast_computer

An exhaustive run can be performed by setting exhaustive to true in the config:

pixi run snakemake -s benchmark/benchmark.smk --cores 20 -d /path/to/working/directory --use-conda --config exhaustive=true

Example

pixi run snakemake -s example/example.smk --cores 20 -d /path/to/working/directory --use-conda

SLURM submission

In case you want to run either the benchmark of the example via slurm, an example profile is included in this repository. Appending --profile slurm-example-config results in jobs being submitted via SLURM rather than being executed locally. Make sure that the settings (queue, mem_mb, runtime, ...) in slurm-example-config/config.yaml are appropriate for your cluster.

Collate figures

The results generated from both workflows (benchmark and example workflow), as well as the code to generate figure 1 are included in this repository. To collate/generate the figures in the figures directory, simply run:

pixi run bash figures/collate_figures.sh

Public data

Both the benchmark as well as the example use publicly available data. The processed version of this data is included in the zenodo archive (and will be downloaded automatically by the respective workflows), the original source data can be retrieved through the accessions listed here.

Purpose	Modality	Organism	SRA	BioProject	GEO	doi
benchmark	ChIP - H3K9me3	Human	SRR28592124	PRJNA1097546	GSE263436	10.1073/pnas.2412258121
benchmark	RNA	Human	SRR28012902	PRJNA1078228	GSE256091	10.1158/0008-5472.CAN-23-1551
benchmark	WGS	Human	SRR15494527	PRJNA752223	/	/
benchmark	ChIP - CENH3	Wheat	SRR1686799	PRJNA268976	GSE63752	10.1105/tpc.19.00133
benchmark	RNA	Wheat	SRR27822150	PRJNA1071712	GSE254797	10.3389/fpls.2024.1401135
benchmark	WGS	Wheat	SRR27887047	PRJNA956839	/	10.1038/s41586-024-07808-z
example	ChIP - H3K27ac wt1	Mouse	SRR15829033	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K27ac wt2	Mouse	SRR15829034	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K27me3 wt1	Mouse	SRR15829036	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K27me3 wt2	Mouse	SRR15829037	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K4me1 wt1	Mouse	SRR15829042	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K4me1 wt2	Mouse	SRR15829043	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K4me3 wt1	Mouse	SRR15829045	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K4me3 wt2	Mouse	SRR15829046	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K9me3 wt1	Mouse	SRR15829048	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K9me3 wt2	Mouse	SRR15829049	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - input wt1	Mouse	SRR15829058	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - input wt2	Mouse	SRR15829059	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	RNA wt1	Mouse	SRR15829077	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	RNA wt2	Mouse	SRR15829078	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ATAC wt1	Mouse	SRR15829121	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ATAC wt2	Mouse	SRR15829122	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	WGBS wt1	Mouse	SRR15829019	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	WGBS wt2	Mouse	SRR15829020	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	RNA ko1	Mouse	SRR15829149	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	RNA ko2	Mouse	SRR15829150	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ATAC wt1	Mouse	SRR15829084	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ATAC wt2	Mouse	SRR15829085	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	WGBS wt1	Mouse	SRR15829089	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	WGBS wt2	Mouse	SRR15829090	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K27ac ko1	Mouse	SRR15829101	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K27ac ko2	Mouse	SRR15829102	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K27me3 ko1	Mouse	SRR15829103	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K27me3 ko2	Mouse	SRR15829104	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K4me1 ko1	Mouse	SRR15829107	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K4me1 ko2	Mouse	SRR15829108	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K4me3 ko1	Mouse	SRR15829109	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K4me3 ko2	Mouse	SRR15829110	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K9me3 ko1	Mouse	SRR15829111	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - H3K9me3 ko2	Mouse	SRR15829124	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - input ko1	Mouse	SRR15829131	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3
example	ChIP - input ko2	Mouse	SRR15829132	PRJNA762170	GSE183764	10.1038/s41586-023-06781-3