Diffuse ChIP-seq coverage island analysis algorithms
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README.md

README.md

supermerge_logo

SUPERmerge

About

SUPERmerge is a ChIP-seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. SUPERmerge is especially useful for investigating low sample size ChIP-seq experiments in which epigenetic histone modifications (e.g., H3K9me1, H3K27me3) result in inherently broad peaks with a diffuse range of signal enrichment spanning multiple consecutive genomic loci and annotated features.

Logo

SUPERmerge evaluates read coverage islands from histone modification ChIP-seq data with broad histone marks, which can often be wide in diameter and low in signal. Just like having a cell phone on an island in the middle of the ocean.

Installation

gcc -o supermerge supermerge.c

Usage

./supermerge –d 20 –i 500 –g gencode.v19.annotation.gtf myFile.bam

See manuscript for details: https://doi.org/10.1101/121897.

Funding

SUPERmerge is supported by the United States Department of Defense (DoD) through the National Defense Science and Engineering Graduate Fellowship (NDSEG) Program. This research was conducted with Government support under and awarded by DoD, Army Research Office (ARO), National Defense Science and Engineering Graduate (NDSEG) Fellowship, 32 CFR 168a.