kdpeak

kdpeak is a Python package designed to identifying genomic peaks from genomic reads in bed format using kernel density estimation (KDE).

Installation

Install via PyPI with:

pip install kdpeak

Alternatively, install directly from GitHub:

pip install git+https://github.com/settylab/kdpeak.git

Using kdpeak

kdpeak allows for processing of a bed file. It applies KDE, pinpoints peaks based on the fragemnt end density, and records the results in an output bed file. The package enables customization of parameters like KDE bandwidth, sequence blacklist, minimum peak size, and others. Designed to deliver a specific fraction-in-peaks (FRiP), it defaults to 0.3.

Elementary usage:

kdpeak reads.bed --frip 0.3 --out peaks.bed

Parameters

usage: kdpeak [-h] [--out OUTPUT_FILE] [-l LEVEL] [--logfile LOGFILE] [--blacklisted-seqs chrN [chrN ...]] [--kde-bw FLOAT] [--min-peak-size INT] [--fraction-in-peaks FLOAT] [--span INT] READS.BED

Positional Argument:

• reads.bed - Path to the bed file containing the genomic reads.

Options:

• -h, --help - Show this help message and exit.
• --out output_file.bed - Path to the output file where the results will be saved. Peaks are saved in bed format with the columns: start, end, peak name, AUC (area under the cut density curve where cut-density is in cuts per 100 base pairs). Defaults to peaks.bed.
• --summits-out summits_file.bed - Path to the output file where the peak summits will be saved. The file will have columns for start, end (start+1), peak name, and summit height (in cuts per 100 base pairs). If nothing is specified the summits will not be saved.
• -l LEVEL, --log LEVEL - Set the logging level. Options include: DEBUG, INFO, WARNING, ERROR, CRITICAL. Default is INFO.
• --logfile LOGFILE - Path to the file to write a detailed log.
• --blacklisted-seqs chrN [chrN ...] - List of sequences (e.g., chromosomes) to exclude from peak calling. Input as space-separated values.
• --kde-bw FLOAT - Bandwidth (standard deviation, sigma in base pairs) for the KDE. Increase for larger features to reduce noise. Default is 200.
• --min-peak-size INT - Minimal size (in base pairs) for a peak to be considered valid. Default is 100.
• --fraction-in-peaks FLOAT, --frip FLOAT - Expected fraction of total reads to be located in peaks. Default is 0.3.
• --span INT - Resolution of the analysis in base pairs, determining the granularity of the KDE and peak calling. Default is 10.

Utilizing All Available Options:

kdpeak reads.bed --out peaks.bed --log DEBUG --logfile debug.log --blacklisted-seqs chr1 chr2 --kde-bw 500 --min-peak-size 50 --frip 0.5 --span 5

Disclaimer

kdpeak, being in its Alpha stage, encourages usage with care. We warmly welcome users to report any issues experienced during utilization. Together, we can enhance kdpeak for a better genomic analysis experience.