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 () | Advanced Peak Shape Tools () | Apply Peak Shape Filter ()
This will open up the wizard shown in figure 34.35 where you can select the input data (e.g. mapped ChIP-Seq reads). Track based read mappings () and stand-alone read mappings () / () 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.
Click Next to go to the next wizard step (shown in figure 34.36).
In this wizard step you have the following options:
- Peak shape filter The peak shape filter () to apply to the data. Peak shape filters can be obtained as the result of the ChIP-Seq Analysis tool. If no filter is given, a filter is derived from the input data.
- Maximum P-value for peak calling The threshold for reporting peaks can be specified by this option.
Click Next to go to the wizard step shown in figure 34.37.
In addition to the annotation track with Peak annotations () that will always be generated by the algorithm, you can choose to select an additional output type:
- Peak shape score () A graph track containing the peak shape score. The track shows the peak shape score for each genomic position. To save disk space, only scores greater than zero are reported. For the definition of peak shape score.
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 (), see Peak track.