Next-Generation Sequencing Data Analysis, 2nd Edition

Mapping Protein-DNA Interactions with ChIP-Seq 307

signicantly higher than that in the surrounding region; or (3) clonal signal,

to remove peaks with high number of reads that map to only a small number

of unique positions. SPP, an R package, calculates smoothed read enrichment

prole along the genome and identies signicantly enriched sites compared

to input control using methods such as WTD (Window Tag Density). The

WTD method considers sequence tag patterns immediately upstream and

downstream of the center of the binding location, thereby increasing predic-

tion accuracy. The peak calling employed in PeakSeq is a two- pass process. In

its rst pass, PeakSeq uses background modeling to identify initial potential

binding regions. ...