Apply Peak Shape Filter

The Apply Peak Shape Filter tool allows you to apply a peak shape filter to sequencing data to discover regions (peaks), which match a given peak shape (see Applying peak shape filters to call peaks).

To run the Apply Peak Shape Filter tool:

        Toolbox | Epigenomics Analysis (Image epigenomics) | Advanced Peak Shape Tools (Image adv_epigenomics) | Apply Peak Shape Filter (Image apply_peak_shape_filter)

This will open up the wizard shown in figure 36.33 where you can select the input data (e.g. mapped ChIP-Seq reads). Track based read mappings (Image read_track_16_n_p) and stand-alone read mappings (Image contig) / (Image multicontig) are both accepted. Multiple inputs are accepted, provided that they refer to the same genome. At least 2 input files must be provided (sample + control for example) if the tool is to be used with a filter that was built from a sample and a control. Note: the order of the inputs should be the same when building the filter and applying the filter, i.e., if the filter was generated from Sample 1 + control, with control being the second object transferred over in the wizard, then when running the Apply Peak Shape Filter tool, the control should also be the second object used in the wizard.

Image PQS_apply_wiz_step1
Figure 36.33: Select the input data for Apply Peak Shape Filter.

Click Next to go to the next wizard step (shown in figure 36.34).

Image PQS_apply_wiz_step2
Figure 36.34: Options for Apply Peak Shape Filter.

In this wizard step you have the following options:

Click Next to go to the wizard step shown in figure 36.35.

Image PQS_apply_wiz_step3
Figure 36.35: Output options for Apply Peak Shape Filter.

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 an additional output type:

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.

For more information on the Peak track (Image annotation_track_16_n_p), see Peak track.