Welcome to Diachromatic’s documentation¶
Differential Analysis of Chromatin Interactions by Capture (Diachromatic)¶
Diachromatic is a Java application that implements a capture Hi-C preprocessing pipeline followed by analysis of differential chromatin interactions (“loopings”). Diachromatic is designed to work with the capture probes as designed by GOPHER.
Generator Of Probes for capture Hi-C Expriments at high Resolution (GOPHER)¶
GOPHER is a Java application designed to help design capture probes for capture Hi-C and related protocols. Capture Hi-C (CHC) is based on the Hi-C protocol but uses capture baits (similar to whole-exome sequencing) to enrich a set of viewpoints. Commonly, the viewpoints represent proximal promoter regions (surrounding the transcription start site [TSS]) of genes of interest or of all protein-coding genes. CHC detects interactions between viewpoint regions and distal enhancers (or other genomic regions) and has been most commonly performed with the 4-cutter DpnII or with the 6-cutter HindIII.