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Keywords {🔍}

data, contact, hic, hicpro, maps, read, genome, pubmed, reads, article, analysis, pairs, map, processing, allelespecific, google, scholar, quality, interactions, valid, chromosome, size, aligned, implementation, resolution, genomewide, cas, ligation, mapping, normalization, iterative, correction, generate, restriction, table, generated, central, pipeline, sequencing, hiclib, chromatin, steps, file, fig, interaction, high, human, expected, products, methods,

Topics {✒️}

high-throughput chromosome capture rna-directed chromosome conformation article download pdf allele-specific interaction products intra-domain chromatin interactions genome-wide contact map chong-jian chen inter-chromosomal contact maps genome-wide interaction matrix genome-wide contact maps single command-line manner allele-specific contact maps intra-chromosomal contact maps discard intra-chromosomal pairs jean-philippe vert inter-chromosomal maps generated normalized intra-chromosomal maps genome-wide sequencing data intra-chromosomal interactions depending pe paired end allele-specific read pairs distinguish allele-specific interactions genome-wide iterative correction full access keywords chromosome conformation cis-regulatory landscape dxz4 micro-satellite 3d map paired-end sequencing reads nucleus search search paired-end reads depending short range contacts hic-pro maps reads chromosomal contact map inter-chromosomal maps mammalian genomes identified fast gapped-read alignment article servant map chromatin interactions sparse matrix-based implementation inter-chromosomal interactions author information authors dimensional chromatin interactome allele-specific maps results hic-pro results paired-end sequencing edith heard related subjects labex deep cancer research institutes

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         description:HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro .
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      description:HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro .
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            name:INSERM U934
            address:
               name:INSERM U934, Paris, France
               type:PostalAddress
            type:Organization
            name:Annoroad Gene Technology Co., Ltd
            address:
               name:Annoroad Gene Technology Co., Ltd, Beijing, China
               type:PostalAddress
            type:Organization
      name:Jean-Philippe Vert
      affiliation:
            name:Institut Curie
            address:
               name:Institut Curie, Paris, France
               type:PostalAddress
            type:Organization
            name:INSERM, U900
            address:
               name:INSERM, U900, Paris, France
               type:PostalAddress
            type:Organization
            name:CBIO-Centre for Computational Biology
            address:
               name:Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
               type:PostalAddress
            type:Organization
      name:Edith Heard
      affiliation:
            name:Institut Curie
            address:
               name:Institut Curie, Paris, France
               type:PostalAddress
            type:Organization
            name:CNRS UMR3215
            address:
               name:CNRS UMR3215, Paris, France
               type:PostalAddress
            type:Organization
            name:INSERM U934
            address:
               name:INSERM U934, Paris, France
               type:PostalAddress
            type:Organization
      name:Job Dekker
      affiliation:
            name:University of Massachusetts Medical School
            address:
               name:Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, USA
               type:PostalAddress
            type:Organization
      name:Emmanuel Barillot
      affiliation:
            name:Institut Curie
            address:
               name:Institut Curie, Paris, France
               type:PostalAddress
            type:Organization
            name:INSERM, U900
            address:
               name:INSERM, U900, Paris, France
               type:PostalAddress
            type:Organization
            name:CBIO-Centre for Computational Biology
            address:
               name:Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
               type:PostalAddress
            type:Organization
PostalAddress:
      name:Institut Curie, Paris, France
      name:INSERM, U900, Paris, France
      name:Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
      name:Institut Curie, Paris, France
      name:INSERM, U900, Paris, France
      name:Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
      name:Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, USA
      name:Sysra, Yerres, France
      name:Institut Curie, Paris, France
      name:INSERM, U900, Paris, France
      name:Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
      name:CNRS UMR3215, Paris, France
      name:INSERM U934, Paris, France
      name:Annoroad Gene Technology Co., Ltd, Beijing, China
      name:Institut Curie, Paris, France
      name:INSERM, U900, Paris, France
      name:Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
      name:Institut Curie, Paris, France
      name:CNRS UMR3215, Paris, France
      name:INSERM U934, Paris, France
      name:Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, USA
      name:Institut Curie, Paris, France
      name:INSERM, U900, Paris, France
      name:Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France

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