Annotated or annotation-free
Use GTF/GFF3 for gene/transcript region labels or omit annotation for whole-genome BAM scanning.
GenomePeak v1.1
Peak calling directly in genome coordinates.
GenomePeak analyzes genome-aligned meRIP-seq / m6A-seq and RIP-seq BAM files. Version 1.1 supports optional GTF/GFF3 annotation as well as annotation-free whole-genome peak discovery.
What it does
GenomePeak workflow.
Purpose-built scientific software with downloadable documentation and reproducible local workflows.
Assay-specific modes
meRIP and RIP modes provide spatial defaults appropriate for broad modification enrichment or narrower RBP footprints.
Bounded genome scanning
Chunked interval processing avoids chromosome-sized coverage arrays.
Shape refinement
Multiscale candidates, local contrast, rescue FDR, prominence, valley and mountain-shape filters refine peaks.
Region annotation
Annotated runs can label UTR, CDS, exon, intron, exon-intron spanning and unannotated contexts.
Browser visualization
Inspect genomic coverage and transcript models and export peak tables and plots.
Usage
CLI example.
GTF/GFF3 is optional in v1.1. Use --scope genome for annotation-free analysis:
genomepeak callpeak \ -t RIP.bam -c Input.bam \ -n HuR --assay rip \ --scope genome \ --outdir HuR_GenomePeak
Install / launch
Start the release locally.
tar -xzf GenomePeak_CLI_v1.1_linux_x86_64.tar.gz cd GenomePeak_CLI_v1.1_linux_x86_64 chmod +x genomepeak ./genomepeak --help
Research-use software. Use BAMs and annotation from the same genome assembly. Annotation-free peaks intentionally do not carry gene assignments.