HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications.

ABSTRACT:

Summary

Folding of eukaryotic genomes within nuclear space enables physical and functional contacts between regions that are otherwise kilobases away in sequence space. Targeted chromosome conformation capture methods (T2C, chi-C and HiCap) are capable of informing genomic contacts for a subset of regions targeted by probes. We here present HiCapTools, a software package that can design sequence capture probes for targeted chromosome capture applications and analyse sequencing output to detect proximities involving targeted fragments. Two probes are designed for each feature while avoiding repeat elements and non-unique regions. The data analysis suite processes alignment files to report genomic proximities for each feature at restriction fragment level and is isoform-aware for gen

SUBMITTER: Anil A 

PROVIDER: S-EPMC6368139 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature