HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

Genome Biology - Tập 16 Số 1 - 2015
Nicolas Servant1, Nelle Varoquaux1, Bryan R. Lajoie2, Éric Viara3, Chong Jian Chen1, Jean-Philippe Vert1, Edith Heard1, Job Dekker4, Emmanuel Barillot5
1Institut Curie, Paris, France
2Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
3Sysra, Yerres, France
4Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
5INSERM, U900, Paris, France

Tóm tắt

Từ khóa


Tài liệu tham khảo

de Wit E, de Laat W. A decade of 3C technologies: insights into nuclear organization. Genes Dev. 2012;26:11–24.

Barutcu AR, Fritz AJ, Sayyed KZ, van Wijnen AJ, Lian JB, Stein JL, et al. C-ing the genome: A compendium of chromosome conformation capture methods to study higher-order chromatin organization. J Cell Physiol. 2015;1097–4652. doi:10.1002/jcp.25062.

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326(5950):289–93. doi: 10.1038/ng.947 .

Ma W, Ay F, Lee C, Gulsoy G, Deng X, Cook S, et al. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of lincRNA genes in human cells. Nat Methods. 2015;12:71–8. doi: 10.1038/nmeth.3205 .

Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, et al. Spatial partitioning of the regulatory landscape of the x-inactivation centre. Nature. 2012;485(7398):381–5. doi: 10.1038/nature11049 .

Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376–80. doi: 10.1038/nature11082 .

Rao SSP, Huntley MH, Durand NC, Bochkov SID, Robinson JT, Sanborn AL, et al. A 3d map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159(7):1665–80. doi: 10.1016/j.cell.2014.11.021 .

Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee Y, et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature. 2013;503(7475):290–4. doi: 10.1038/nature12644 .

Lajoie BR, Dekker J, Kaplan N. The hitchhiker’s guide to hi-c analysis: Practical guidelines. Methods. 2015;72:65–75. doi: 10.1016/j.ymeth.2014.10.031 .

Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Lasio P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576–89. doi: 10.1016/j.molcel.2010.05.004 .

HiCUP. http://www.bioinformatics.babraham.ac.uk/projects/hicup/ .

Castellano G, Le Dily F, Hermoso Pulido A, Beato M, Roma G. Hi-Cpipe: a pipeline for high-throughput chromosome capture. bioRxiv 2015. Cold Spring Harbor Labs Journals. doi: 10.1101/020636 .

Schmid Marc W, Schmid MW, Grob S, Grossniklaus U. HiCdat: a fast and easy-to-use Hi-C data analysis tool. BMC Bioinformatics. 2015;16:277. doi: 10.1186/s12859-015-0678-x .

HiCbox. https://github.com/koszullab/HiC-Box .

SNPsplit. http://www.bioinformatics.babraham.ac.uk/projects/SNPsplit/ .

Hsieh TS, Weiner A, Lajoie B, Dekker J, Friedman N, Rando O. Mapping nucleosome resolution chromosome folding in yeast by micro-C. Cell. 2015;162(1):108–19. doi: 10.1016/j.cell.2015.05.048 .

Imakaev M, Fudenberg G, Patton McCord R, Naumova N, Goloborodko A, Lajoie BR, et al. Iterative correction of hi-c data reveals hallmarks of chromosome organization. Nat Methods. 2012;9(10):999–1003. doi: 10.1038/nmeth.2148 .

Yaffe E, Tanay A. Probabilistic modelling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet. 2011;43(11):1059–65. doi: 10.1038/ng.947 .

Hu M, Deng K, Selvaraj S, Qin Z, Ren B, Liu J. HiCNorm: removing biases in Hi-C data via poisson regression. Bioinformatics. 2012;28(23):3131–3. doi: 10.1093/bioinformatics/bts570 .

Li W, Gong K, Li Q, Alber Fand Zhou XJ. Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale hi-c data. Bioinformatics. 2015;31(6):960–2. doi: 10.1093/bioinformatics/btu747 .

Minajigi A, Froberg JE, Wei C, Sunwoo H, Kesner B, Colognori D, et al. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Science. 2015;349(6245):aab2276. doi: 10.1126/science.aab2276 .

Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, et al. Bipartite structure of the inactive mouse X chromosome. Genome Biol. 2015;16:152. doi: 10.1186/s13059-015-0728-8 .

Selvaraj S, Dixon JR, Bansal V, Ren B. Whole-genome haplotype reconstruction using proximity-ligation ans shotgun sequencing. Nat Biotechnol. 2013;31(12):1111–8. doi: 10.1038/nbt.2728 .

Platinum Illumina Genomes Project. http://www.illumina.com/platinumgenomes/ .

Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2.

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie2. Nat Methods. 2012;9:357–9. doi: 10.1038/nmeth.1923 .

Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J. Normalization of a chromosomal contact map. BMC Genomics. 2012;13:436. doi: 10.1186/1471-2164-13-436 .

Servant N, Lajoie BR, Nora EP, Giorgetti L, Chen CJ, Heard E, et al. HiTC: Exploration of high-throughput ‘C’ experiments. Bioinformatics. 2012;28(21):2843–4.