CLC Genomics Workbenchcan perform analysis of Chromatin immunoprecipitation sequencing (ChIP-Seq) data based on the information contained in a single sample subjected to immunoprecipitation (ChIP-sample) or by comparing a ChIP-sample to a control sample where the immunoprecipitation step is omitted. The first step in a ChIP-Seq analysis is to Map reads to reference which maps your reads against one or more specified reference sequences. If both a ChIP- and a control sample is used, these must be mapped separately to produce separate ChIP- and control samples. These samples are then used as input to the ChIP-Seq tool which surveys the pattern in coverage to detect significant peaks:
Toolbox | Epigenomics Analysis () | ChIP-Seq Analysis ()
This opens a dialog where you can select one or more mapping results ()/ () to use as ChIP-samples. Control samples are selected in the next step.