HIPPIE: A High-Throughput Identification Pipeline for Promoter Interacting Enhancer elements
Introduction
HIPPIE is the workflow for analyzing batches of Hi-C paired-end reads in compressed FASTQ format (.fastq.gz) and predict enhancer–target gene interactions. HIPPIE streamlines the entire processing phase including reads mapping, quality control and enhancer–target gene prediction as well as characterizing the interactions.
Access HIPPIE
*The test fastq.gz files consist mainly chromosome1 and chromosome2 reads from an original Hi-C experiment (Lieberman-Aiden et al. Science 2009) GEO accession: GSM455139 and GSM455140.
Credits
If you use HIPPIE for your research, please use the following citation:
Hwang Y.-C., Lin C.-F., Valladares O., Malamon J., Kuksa P. P., Zheng Q., Gregory B. D., and Wang L.-S.. HIPPIE: A high-throughput identification pipeline for promoter interacting enhancer elements. (2014, Bioinformatics) [DOI:10.1093/bioinformatics/btu801]
Release Notes
[2015/04/26] Release of HIPPIE v0.0.2-beta. Major changes:
- We replaced BWA by STAR for read mapping. HIPPIE now supports (a) identdifying chimeric reads, and (b) faster mapping.
- The interaction hotspot calling option is deprecated in this version, and HIPPIE now only supports calling interactive unit using restriction fragment-based. If you wish to use hotspot and extended hotspot calling, please download the previous release v0.0.1-beta.
- The setup of input directory structure. For detail, please read the corresponding user manual.
There are also some minor fixing to improve the pipeline efficiency.
[2015/03/16] First release of HIPPIE v0.0.1-beta.
[2014/05/08] Website created and source code released.
Licensing
HIPPIE is released under the MIT license and is available for academic and nonprofit use for free.
[Last update: 2015/4/26]