Running the Transcription Factor ChIP-Seq tool

To run the Transcription Factor ChIP-Seq tool:

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

This will open up the wizard shown in figure 36.9 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 36.9: Select the input data for the Transcription Factor ChIP-Seq tool.

Click Next to go to the next wizard step (shown in figure 36.10).

Image PQS_chipseq_step2
Figure 36.10: Options for the Transcription Factor ChIP-Seq tool.

In this wizard step you have the following options:

Click Next to go to the wizard step shown in figure 36.11.

Image PQS_chipseq_step3
Figure 36.11: Output options for the Transcription Factor ChIP-Seq tool.

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.