HiCUP now uses CIGAR string information when positioning reads to restriction fragments and during the de-duplication process.

The script hicup_truncater used to incorporate such Ns into the FASTQ truncated read.

Fixed bug when specifying a cut-site containing an N (any nucleotide).

Click here for notes on all releases Version 0.8.0 onwards.

Systems now need R and the R modules Tidyverse and Plotly installed See documentation for further details

Compatible with restriction enzyme/sonication or restrictionĬhangelog Attention: HiCUP 0.8.0 has major changes to the report summary generation.

Reads map to the same restriction fragment

Filters data to remove common artefacts e.g.

Pairs forward and reverse reads for each di-tag, producing output.

Maps each read end independently using parameters.Truncates accordingly with a view to improving mapping efficiency Identifies putative Hi-C junctions in sequence reads and.Used to assess the quality of the data and help improve the construction It will also produce a set of metrics which can be HiCUP is designed to take the raw sequence output from a HiC experimentĪnd produce a filtered set of mapped interaction pairs, suitable for Of products that were spatially close to each other in the nucleus. The DNA is then digested and ligated to generate a library The Hi-C protocol involves formaldehyde-fixingĬells to create DNA-protein bonds that cross-link interacting DNA Hi-C, developed from 3C, identifies long-range genomic R (with modules Tidyverse and Plotly installed)īeta - HiCUP is routinely being used to process real data, however it is still under active development.įull documentation and audio-visual demonstrations are available by clicking here A tool for mapping and performing quality control on Hi-C data

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