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| Status |
Public on Oct 29, 2015 |
| Title |
HiCUP: pipeline for mapping and processing Hi-C data |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
HiCUP is a pipeline for processing sequence data generated by Hi-C, a technique used to investigate the three-dimensional organisation of a genome. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequent analysis. HiCUP also provides an easy-to-interpret yet detailed quality control report that may be used by researchers to refine their experimental protocol for future studies. The software is freely available and has already been used for processing Hi-C data in several recently published peer-reviewed research articles. This experiment investigates the impact of using HiCUP to remove putative PCR amplification products in heavily duplicated Capture Hi-C libraries.
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| |
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| Overall design |
Examination of three Capture Hi-C libraries
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| |
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| Contributor(s) |
Wingett SW, Ewels PA, Furlan-Magaril M, Nagano T, Schoenfelder S, Fraser P, Andrews S |
| Citation(s) |
26835000 |
| Submission date |
Sep 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Steven William Wingett |
| E-mail(s) |
steven.wingett@mrc-lmb.cam.ac.uk
|
| Organization name |
MRC Laboratory of Molecular Biology
|
| Department |
Cell Biology
|
| Street address |
Francis Crick Avenue, Cambridge Biomedical Campus
|
| City |
Cambridge |
| State/province |
Cambs |
| ZIP/Postal code |
CB2 0QH |
| Country |
United Kingdom |
| |
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| Platforms (1) |
| GPL15103 |
Illumina HiSeq 1000 (Mus musculus) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA296367 |
| SRA |
SRP063864 |
