te_hic Hi-C analysis software implementation

Transposable elements (TEs) occupy nearly half of the human genome and play diverse biological roles. Despite their abundance, the extent to which TEs contribute to three-dimensional (3D) genome structure remains unclear. To investigate this, we generate a modified Hi-C analysis pipeline to probe TE-associated chromatin interactions. One of the first steps in HiC analysis is to discard multimapping reads, low quality mapping reads, or otherwise disregard repeat regions of the genome. We believe this is a mistake when you consider that most of the genome consists of badly mapping repeats. This is a tool that aims to fill that gap by looking at HiC data from the perspective of TEs.

This repository contains a copy of the code for te_hic, downloaded from https://github.com/oaxiom/te_hic on 2025/12/18.