Score Regions

The Score Regions tool allows you to apply a new peak shape filter to score genomic regions according how they match a given peak shape.

To run the Score Regions tool:

        Toolbox | Epigenomics Analysis (Image epigenomics) | Advanced Peak Shape Tools (Image adv_epigenomics) | Score Regions (Image score_regions)

This will open up the wizard shown in figure 33.38 where you can select the input data (e.g. mapped ChIP-Seq reads). Multiple inputs 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_score_wiz_step1
Figure 33.38: Select the input data for Score Regions.

Click Next to go to the next wizard step (shown in figure 33.39).

Image PQS_score_wiz_step2
Figure 33.39: Options for Score Regions.

In this wizard step you have the following options:

The result of the algorithm will be an annotation track (Image annotation_track_16_n_p) of the same type as the regions to score annotation track, where the columns of type Peak shape score, P-value and Center of peak will be added or replaced.

After clicking Next, you can choose whether you want to open the result 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.