Running the ChIP-Seq Analysis tool

To run the ChIP-Seq Analysis tool:

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

This will open up the wizard shown in figure 30.5 where you can select the input data (the mapped ChIP-seq reads). Multiple inputs (e.g. replicate experiments) are accepted, provided that they refer to the same genome. Track based read mappings (Image read_track_16_n_p) and stand-alone read mappings (Image contig) / (Image multicontig) are both accepted.

Image PQS_chipseq_step1
Figure 30.5: Select the input data for ChIP-Seq Analysis.

Click on the button labeled Next to go to the next wizard step (shown in figure 30.6).

Image PQS_chipseq_step2
Figure 30.6: Options for ChIP-Seq Analysis.

In this wizard step you have the following options:

Click on the button labeled Next to go to the wizard step shown in figure 30.7.

Image PQS_chipseq_step3
Figure 30.7: Output options for ChIP-Seq Analysis.

In addition to the annotation track with Peak annotations (Image annotation_track_16_n_p) that will always be generated by the algorithm, you can choose to select additional output types.

The options are:

Choose whether you want to open the results directly, or save the results in the Navigation Area. If you choose to save the results, you will be asked to specify where you would like to save them.