HomeCLC FAQ - Analyses-related questionsRead mappingHow can I identify low or zero coverage regions in a mapping?

5.6. How can I identify low or zero coverage regions in a mapping?

If you have a read mapping in track format, you could do the following to get gap regions annotated by using this tool:

Toolbox | Track Tools | Graphs | Create Mapping Graph Track

followed by this tool:

Toolbox | Track Tools | Graphs | Identify Graph Threshold areas

where you can set the minimum and maximum coverage to look for. This tool will then generate an annotation track of those regions.

These tools are described in our manual here:




Below is an image of a track list including a read mapping  track and the track outputs of the tools above, where the aim was to identify zero coverage areas in the mapping. 


By opening the track containing the low coverage annotations in table view, you can see information, like the coordinates of the annotations. From within a track list, you can open a particular annotation track in table view by just double clicking on the name of the track. If you open just the track, not within a track list, just click on the little icon that looks like a table at the bottom of the view.

You may also be interested in the Coverage Analysis tool. This does something somewhat different, but may still be of interest. It is described in our manual here:


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