madetunj/peaksanno

Annotate the location of peaks in terms of important genomic features

PEAKS ANNOTATION

DESCRIPTION

Genic annotation of peaks including promoters, gene bodies, gene-centric windows, and proximal genes.

PeaksAnno provides the genic annotation of peaks at promoters, gene bodies, and gene-centric windows. Annotated regions are collated to give a binary overview of proximal genes, and the peak occupancy percentages are graphically presented in a bar plot. This is a part of the major analysis for ChIPSeq or Cut&Run-Seq using our comprehensive pipeline SEASEQ.

USAGE

peaksanno.py -p ["PEAK bed"] [-s ["MACS Summit bed"]] -g ["GTF"] -c ["CHROM SIZES"]

INPUT

The script requires the following files:

1. Peaks bed file
2. GTF/GFF/GFF3 having either gene or transcript (preferred) annotation
3. UCSC provided chromosomal sizes file

An optional summit file from MACS can be included

OUTPUT

PeaksAnno genes the following files:

1. TSS nearest the center of peaks in centerofpeaks_closest.regions.txt.
2. Peaks overlapping genes regions in peaks_within_genebody.regions.txt.
3. Peaks overlapping promoters in peaks_within_promoter.regions.txt.
4. Peaks overlapping windows in peaks_within_window.regions.txt.
5. Peaks identified in previous overlapping regions and comparison of all regions in peaks_compared_regions.peaks.txt.
6. Genes identified in previous overlapping regions and comparison of all regions in peaks_compared_regions.genes.txt.
7. Distribution graphs in peaks_compared_regions.distribution.pdf.

DEFINITIONS

- TSS: TSS (transcription start site)
- promoters: 1kb +/- TSS
- window: 10kb upstream to 3kb downstream of the gene locus
- genebody: 1kb upstream of TSS to TES (transcription end site)

DEPENDENCIES

1. bedtools
2. python3

CITATION

If you are using PEAKSANNO, please cite its parent paper : Adetunji, M.O., Abraham, B.J. SEAseq: a portable and cloud-based chromatin occupancy analysis suite. BMC Bioinformatics 23, 77 (2022). https://doi.org/10.1186/s12859-022-04588-z

CONTACT

Please use the GitHub issues page for reporting any issues/suggestions (recommended).

Alternatively, you can e-mail Modupe Adetunji [email protected]