ChIP sequencing

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 (Image epigenomics) | ChIP-Seq Analysis (Image chip_sequencing)

This opens a dialog where you can select one or more mapping results (Image contig)/ (Image multicontig) to use as ChIP-samples. Control samples are selected in the next step.