ChIP-seq, a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. MACS is a Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa).
- callpeak: call peaks from BAM
- bdgpeakcall: call peaks from BED
- bdgbroadcall: call broad peaks from BED