# HiC Trans Cis Quantitation

The trans cis quantitation method simply works out the percentage of HiC ends for each probe which fall into a trans location. Completely randomly ligated data will generally have a high trans component (anything up to 90%), and this will fall to around 50% for good real HiC datasets - though the exact values will vary depending on the number and size of the chromosomes in the genome.

## Options

The options you have for this module are:

1. Whether you want to count far-cis interactions with the trans hits. If you choose this option you can select the distance over which cis pairs will be counted as trans (the default is 10Mbp).
2. Whether you want to remove duplicate HiC pairs when counting.
3. Whether you'd like to see the final values with the median value for the associated chromosome subtracted. Different chromosomes will have different biases for trans percentages due to their differing lengths. Subtracting the median chromosome value allows you to better see any positional variation in the trans percentage.