# The Feature Probe Generator

The feature probe generator allows to to design probes around a class of annotation features. You can design in different locations around the feature as you can select between making a probe over the feature, upstream of it, downstream of it or centered on it.

The feature probe generator is useful when you are only interested in probes which relate to features.

## Options

The options you can set for this generator are:

1. The class of feature against which you want to design probes
2. If you want to split your feature into subfeatures. If you select this then you will get a set of probes for each exon in a multi-exon feature such as mRNA. If two mRNAs share a common exon then you will get duplicate probes generated.
3. If you want to remove exact duplicate probes. If you have exactly duplicated features then this will leave only one copy of each. This can be useful when designing probes around exons in mRNA features for example.
4. If you want to ignore any strand information which is present on the features you're using. If you select this then each feature, and the associated probes will be assigned the unknown strand. This will affect the position of upstream and downstream probes for features assigned to the reverse strand, and since this will pass through to the probes generated it will also affect directional analyses such as the probe trend plot.
5. What type of probe you want to generate (upstream, downstream, over the feature or centred on it
6. The amount of space you want to add at the end of the type of region you defined. If you have selected anything other than 'Over the feature' you will need to change either the start or end value here or you'll end up with 1bp probes
7. If you want to design a probe within the feature. The first value is relative to the 5-prime end of the feature and the second value is relative to the 3-prime end of the feature, so -100 to +200 would be from 100bp upstream of the feature to 200bp downstream
8. If you want to design a downstream probe. If you do then you can set the downstream region you wish to use. The origin is the end of the 3-prime end of the feature, so -500 to +100 would be 500bp upstream of the end to 100bp downstream