Anchor Modes

To calculate whether a pair is within a specific window of size w and to interpret predicted preferred distances, it is important to define an anchor point from which the distance is measured. TF-COMB supports three different anchor modes: inner, outer and center. The default mode is inner.

  1. inner (default) is the distance between the transcription factors, it is measures as \(start(TF B) - end(TF A)\) . If for example transcription factor B is directly adjacent to Transcription factor A, the difference will be zero.

  2. center is the distance measured from mid of transcription factor to mid of transcription factor \(center(TF B) - center (TF A)\)

  3. outer (uncommonly used) is the distance measured including both transcription factors. \(end(TF B) - start(TF A)\)

Explanatory figure for anchor modes

Created with BioRender.com.