The legacy ChIP-Seq analysis functionality was part of the CLC Genomics Workbench Epigenomics Analysis tools up until version 7.5 where it was replaced by a new ChIP-Seq analysis tool (the former Peak Shape ChIP-Seq Analysis Plugin).
The ChIP-Seq Analysis (legacy) tool can 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 the reads to a reference (see 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.
A stand-alone read mapping is 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.
Please note that stand-alone read mappings, not track-based mappings, are used as input to the Chip-seq tool. In addition, the read mapping must be carried out using a reference that is a sequence () or sequence list (). Track-based () sequences can not be used as references for mappings that will be used for Chip-seq analyses. The reason for this is that sequence and sequence list objects can contain annotations and these are included in a read mapping where the annotated sequence or sequence list reference was used. These annotations are important for the current Chip-seq analysis functionality. Annotations for track-based references are held in separate tracks, and this is not yet supported for Chip-seq analysis.
Toolbox | Legacy Tools () | ChIP-Seq Analysis (legacy) ()
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.