Software for ChIP-Seq Analysis utilizing Multi-reads

This page provides softwares & tutorials for

Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick E, Dewey C, and Keles S (2010).
“Discovering transcription factor binding sites in highly repetitive regions of genomes
with multi-read analysis of ChIP-seq data”.


Multi-reads are the reads that map to multiple locations on the reference genome.
Current state of the art for analyzing ChIP-seq data relies on using only reads that
map uniquely to relevant reference genome (uni-reads). This can lead to the omission
of up to 30% of alignable reads. Chung et al. (2010) illustrated that incorporation of
multi-reads significantly increases sequencing depths, leads to detection of novel peaks
that are not otherwise identifiable with uni-reads, and improves detection of peaks
in low mappable regions. The computational and experimental results established that
multi-reads can be of critical importance for studying transcription factor binding
in highly repetitive regions of genomes with ChIP-seq experiments.

Work-flow of ChIP-seq analysis utilizing multi-reads
provides overview of work-flow of ChIP-seq analysis using multi-reads.

ChIP-Seq Analysis Work-flow

1. Download required files & scripts.

2. Align reads & allocate multi-reads.

3. Preprocess CSEM output, mappability, GC content, & ambiguity score files.

4. Call peaks using MOSAiCS.

If you have any questions regaring softwares & tutorials,
please e-mail Dongjun Chung at chungdon_at_stat_dot_wisc_dot_edu.