The Feature Percentile Probe Generator

The feature percentile probe generator is a way to place a set of equally spaced and sized probes over the length of a set of features. It can be useful if you're trying to quantitatively assess an effect which changes over the length of a feature.

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 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.
4. How many probes you want to generate per feature
5. The type of probes you want to make. Proportional probes will fill the entire area of the feature, but the probes from different features will be different lengths. Fixed probes will be the same length for all features. Their centres will be spread evenly over the length of the feature but depending on the overall feature length they may overlap or be separated from each other
6. If you use a fixed length probe you can choose whether you want to place probes at the very start and end of the features
7. If you use a fixed length probe you can specify the probe length you want to use