Genetrap quantitation pipeline

This pipeline is specialised for use in GeneTrap experiments. It takes in a feature track of spliced features and does a read count quantitation. The unusual aspect of the pipeline is that it will only count a read against a feature if either:

1. It overlaps with an exon of that feature, or
2. It sits within an intron, but in the same orientation as the feature

Options

The options you can set for this pipeline are:

1. Which type of feature you want to quantitate
2. Whether to generate raw counts, or have counts which are normalised by total count
3. Whether to log transform the counts