# The Transcription termination quantitation pipeline

The transcription termination quantitation pipeline aims to measure the degree of sequence loss at a putative transcription termination point. The pipeline creates a pair of probes upstream and downstream of the end of an mRNA feature and measures the degree of read count loss at the termination point.

The pipeline generates a single probe covering the whole of the upstream/downstream region (centered on the termination point) and quantitates this with the percentage sequence count loss (100 - ((downstream / upstream) * 100)).

## Options

The options you can set for this pipeline are:

1. The feature type to use for this analysis. This will default to mRNA if an mRNA track exists in your genome, but can be changed to whichever transcript feature track is appropriate
2. The type of library you are quantitating. Some RNA-Seq libraries are strand specific and in these cases the pipeline can ignore reads coming from the wrong strand. You can also choose between strand specific libraries which produce reads on the same strand as the feature or the opposing strand.
3. What the minimum count in the upstream region should be for you to want to calculate a percentage loss. Features which fall below this threshold will be given a null value
4. What the size of the window you're going to place upstream and downstream of the termination point is going to be.