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HiCUP (Hi-C User Pipeline)

Function A tool for mapping and performing quality control on Hi-C data
Language Perl
Requirements Bowtie or Bowtie2
Perl
R (tested with version 3.1.2) [optional]
SAMtools (version 0.1.18 or later)
Unix-based operating system
gzip
Code Maturity Beta - HiCUP is routinely being used to process real data, however it is still under active development.
Code Released Yes, under GNU GPL v3 or later.
Initial Contact Steven Wingett
Full Documentation Full documentation and audio-visual demonstrations are available by clicking here

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Hi-C, developed from 3C, identifies long-range genomic interactions.  The Hi-C protocol involves formaldehyde-fixing cells to create DNA-protein bonds that cross-link interacting DNA loci.  The DNA is then digested and ligated to generate a library of products that were spatially close to each other in the nucleus.

HiCUP is designed to take the raw sequence output from a HiC experiment and produce a filtered set of mapped interaction pairs, suitable for subsequent analysis. It will also produce a set of metrics which can be used to assess the quality of the data and help improve the construction of future libraries.

Main features:

Changelog