The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis
It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (chromosome conformation capture) and its derived methods are now widely applied to investigate three-dimensional (3D) genome organizations and gene regulation....
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| Veröffentlicht in: | Genes 2020-03, Vol.11 (3), p.289 |
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| creator | Hong, Ping Jiang, Hao Xu, Weize Lin, Da Xu, Qian Cao, Gang Li, Guoliang |
| description | It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (chromosome conformation capture) and its derived methods are now widely applied to investigate three-dimensional (3D) genome organizations and gene regulation. Digestion-ligation-only Hi-C (DLO Hi-C) is a new technology with high efficiency and cost-effectiveness for whole-genome chromosome conformation capture. Here, we introduce the DLO Hi-C tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and for providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied the DLO Hi-C tool to different DLO Hi-C datasets and demonstrated its ability in processing large data with multithreading. The DLO Hi-C tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing. |
| doi_str_mv | 10.3390/genes11030289 |
| format | Article |
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Digestion-ligation-only Hi-C (DLO Hi-C) is a new technology with high efficiency and cost-effectiveness for whole-genome chromosome conformation capture. Here, we introduce the DLO Hi-C tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and for providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied the DLO Hi-C tool to different DLO Hi-C datasets and demonstrated its ability in processing large data with multithreading. The DLO Hi-C tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes11030289</identifier><identifier>PMID: 32164155</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Chromatin Assembly and Disassembly ; Chromosomes - chemistry ; Chromosomes - genetics ; Conformation ; Costs and Cost Analysis ; Data analysis ; Data processing ; Deoxyribonucleic acid ; Design ; DNA ; Gene expression ; Gene mapping ; Gene regulation ; Genomes ; Genomics - economics ; Genomics - methods ; Genomics - standards ; Humans ; Java ; Methods ; Noise ; Pipelines ; Programming languages ; Regulatory sequences ; Whole Genome Sequencing - economics ; Whole Genome Sequencing - methods ; Whole Genome Sequencing - standards</subject><ispartof>Genes, 2020-03, Vol.11 (3), p.289</ispartof><rights>2020. This work is licensed under http://creativecommons.org/licenses/by/3.0/ (the “License”). 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It is convenient and efficient for DLO Hi-C data processing.</description><subject>Chromatin Assembly and Disassembly</subject><subject>Chromosomes - chemistry</subject><subject>Chromosomes - genetics</subject><subject>Conformation</subject><subject>Costs and Cost Analysis</subject><subject>Data analysis</subject><subject>Data processing</subject><subject>Deoxyribonucleic acid</subject><subject>Design</subject><subject>DNA</subject><subject>Gene expression</subject><subject>Gene mapping</subject><subject>Gene regulation</subject><subject>Genomes</subject><subject>Genomics - economics</subject><subject>Genomics - methods</subject><subject>Genomics - standards</subject><subject>Humans</subject><subject>Java</subject><subject>Methods</subject><subject>Noise</subject><subject>Pipelines</subject><subject>Programming languages</subject><subject>Regulatory sequences</subject><subject>Whole Genome Sequencing - economics</subject><subject>Whole Genome Sequencing - methods</subject><subject>Whole Genome Sequencing - standards</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNpdkc1LAzEQxYMoKtWjV1nw4mU1n032IsjWLyj0Us9xupvdRnY3NdkV-t8bW5XWOWQG5sdjXh5CFwTfMJbh29p0JhCCGaYqO0CnFEuWck7F4c58gs5DeMexOKYYi2N0wigZcyLEKXqbL00ymc6SZ5vmydy5JqmcTya2NqG3rkuntobNMOua9ZbKl961LrjWJLnrIt5uiCSHVT_4KAc9JPcdNOtgwxk6qqAJ5vynj9Dr48M8f06ns6eX_H6aFlyRPuXFQgLlsiRjUIxmRIEEUBJLongWtxwTwmiZVZJWBEQhoBwrrjKxqOhYYjZCd1vd1bBoTVmYrvfQ6JW3Lfi1dmD1_qazS127Ty0Jx4qKKHD9I-DdxxDd69aGwjQNdMYNQVMmJYsfHd8RuvqHvrvBR8NbKgZCBYlUuqUK70Lwpvo7hmD9HZ_eiy_yl7sO_ujfsNgXczuUVA</recordid><startdate>20200310</startdate><enddate>20200310</enddate><creator>Hong, Ping</creator><creator>Jiang, Hao</creator><creator>Xu, Weize</creator><creator>Lin, Da</creator><creator>Xu, Qian</creator><creator>Cao, Gang</creator><creator>Li, Guoliang</creator><general>MDPI AG</general><general>MDPI</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-4844-4455</orcidid><orcidid>https://orcid.org/0000-0003-0585-821X</orcidid><orcidid>https://orcid.org/0000-0003-1601-6640</orcidid></search><sort><creationdate>20200310</creationdate><title>The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis</title><author>Hong, Ping ; 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| subjects | Chromatin Assembly and Disassembly Chromosomes - chemistry Chromosomes - genetics Conformation Costs and Cost Analysis Data analysis Data processing Deoxyribonucleic acid Design DNA Gene expression Gene mapping Gene regulation Genomes Genomics - economics Genomics - methods Genomics - standards Humans Java Methods Noise Pipelines Programming languages Regulatory sequences Whole Genome Sequencing - economics Whole Genome Sequencing - methods Whole Genome Sequencing - standards |
| title | The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis |
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