User:Gcastellano

README

About

High-throughput conformation capture (Hi-C) allows to study the three-dimensional architecture of whole genomes through the detection of long range chromosomal interactions. We developed Hi-Cpipe, a bioinformatics pipeline to facilitate the analysis of HiC dataset. Our tools performs read alignment, filtering of the reads that are in the DNA fragment size window around the restriction enzyme sites, counting of interactions with a user-defined resolution, and generation of contact matrix and heatmaps with a complete mapping of the interaction in the reference genome. Hi-Cpipe is publicly available open source, and can be used for paired-end sequencing from different platforms.

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Authors

MACS is written by Giancarlo Castellano, François Le Dily1, Antoni Hermoso Pulido1 and Guglielmo Roma from Bioinformatics Core and Miguel Beato's Lab @ CRG. Source Code

Citation

Our paper has been published in . Please cite "Castellano et al. Hi-Cpipe: a pipeline for high-throughput chromosome capture. "(2011) vol. pp.".

License This software is distributed under the terms of Artistic License.

Contact If you have any comments, suggestions, questions, bug reports, etc, feel free to contact: Guglielmo.Roma@gmail.com or Giancarlo.Castellano@gmail.com. And PLEASE attach your command line and log messages if possible.

If you think your question/comment may be interesting to the Hi-Cpipe user group, please post it to our "" group.