ChIP sequencing

CLC Genomics Workbenchperform 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 are used, these must be mapped separately to produce separate ChIP- and control samples. Note that read mappings must be done against a reference that is a sequence (Image dna) or sequence list (Image sequencelist) object. ChIP-Seq analysis is not track compatible at this time. This means that track-based (Image sequence_track) sequences can not be used as references. The reason for this is that sequence and sequence list objects can contain annotations. Such annotations will then be carried through to read mappings involving that reference. Track-bases sequences do not contain annotations.

Read mappings can then used as input to the ChIP-Seq tool, which surveys the pattern in coverage to detect significant peaks. Annotations on the reference in the read mapping are carried through to any subsequent ChIP-Seq analysis results.

        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.