Difference between revisions of "Hicup"
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|sw summary=A mapping pipeline for HiC interaction data. Performs independent mapping on each end of the interaction pair and removes commonly found artefacts. | |sw summary=A mapping pipeline for HiC interaction data. Performs independent mapping on each end of the interaction pair and removes commonly found artefacts. | ||
|bio domain=Epigenomics | |bio domain=Epigenomics | ||
| − | |bio method= | + | |bio method=Read mapping, |
| − | |bio tech=Illumina, Ion Torrent, | + | |bio tech=Illumina, Ion Torrent, |
| + | |interface=Command line, | ||
| + | |resource type=Command-line tool, | ||
|created by=Steven Wingett | |created by=Steven Wingett | ||
| − | |created at=The Babraham Institute, | + | |created at=The Babraham Institute, |
|maintained=Yes | |maintained=Yes | ||
| − | |input format=FASTQ, (Compressed) FASTQ, | + | |input format=FASTQ, (Compressed) FASTQ, |
| − | |output format=SAM/BAM, | + | |output format=SAM/BAM, |
| − | |language=Perl, | + | |language=Perl, |
| − | |licence=GPLv3, | + | |licence=GPLv3, |
| − | |os=UNIX, Linux, Mac OS X, | + | |os=UNIX, Linux, Mac OS X, |
}} | }} | ||
== Description == | == Description == | ||
Latest revision as of 15:29, 3 November 2016
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Application data |
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| Created by | Steven Wingett |
|---|---|
| Biological application domain(s) | Epigenomics |
| Principal bioinformatics method(s) | Read mapping |
| Technology | Illumina, Ion Torrent |
| Created at | The Babraham Institute |
| Maintained? | Yes |
| Input format(s) | FASTQ, (Compressed) FASTQ |
| Output format(s) | SAM/BAM |
| Programming language(s) | Perl |
| Interface type(s) | Command line |
| Resource type(s) | Command-line tool |
| Licence | GPLv3 |
| Operating system(s) | UNIX, Linux, Mac OS X |
Summary: A mapping pipeline for HiC interaction data. Performs independent mapping on each end of the interaction pair and removes commonly found artefacts.
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Description
Hicup is a mapping pipeline specifically designed to process HiC interaction data. HiC libraries comprise linked pairs of sequences (di-tags) from separate parts of the genome which were physically close together when the library was created.
The Hicup pipeline separates the two tags and maps them independently to remove any potential bias from the normal paired end mapping mode of normal aligners. It then re-pairs the reads, and filters out common contaminants (linear sequences, circularised fragments, fragments from incomplete digestion etc). The final output is a normal SAM/BAM file of clean HiC data suitable for downstream analysis.
Links
References
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