The Running Window Probe Generator

The running window probe generator generates a set of probes at regular intervals over your genome. It is probably the most commonly used probe generator.

The running window probe generator is useful when you want to be able to identify regions of interest in an unbiased way from any point over your genome.

Options

The options you can set for this generator are:

1. The size of the window you want to use. SeqMonk will automatically look at your data and suggest a size which has a median of 10 reads per window. If you have defined any data groups then it will look only at the groups otherwise it will look at all of your data sets. You can of course change this if you prefer to use a higher or lower value
2. The distance between the start of adjacent windows. By default this value will be the same as the window size such that adjacent windows follow on immediately from each other. If you want your windows to overlap then you should set this value to a size which is smaller than your window size.
3. Instead of using the whole genome to define probes you can choose to make windows inside a more constrained region. This can either be an existing probe list, or it can be the region which is currently visible in the chromosome view.