scholarly journals capC-MAP : A Software Package for Analysis of Capture-C data

2018 ◽  
Author(s):  
Adam Buckle ◽  
Nick Gilbert ◽  
Davide Marenduzzo ◽  
Chris A. Brackley
Keyword(s):  
Data Processing ◽  
Software Package ◽  
Ease Of Use ◽  
Data Capture ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Capture Method

AbstractWe present capC-MAP, a software package for the analysis of Capture-C data. Capture-C is a “many-to-all” chromosome-conformation-capture method. We summarise the method, then detail capC-MAP, the first software specifically designed and optimised for Capture-C data. capC-MAP has been developed with ease-of-use and flexibility in mind: the entire pipe-ine can be run with a single command, or the component programs can be run individually for custom data processing, in a strategy that will suit computational as well as experimental researchers. Finally, we compare and benchmark capC-MAP against another package which can perform (though is not optimised for) analysis of Capture-C data.

A statistical model of intra-chromosome contact maps

Soft Matter ◽  
2015 ◽  
Vol 11 (5) ◽  
pp. 1019-1025 ◽  
Author(s):  
Leonid I. Nazarov ◽  
Mikhail V. Tamm ◽  
Vladik A. Avetisov ◽  
Sergei K. Nechaev
Keyword(s):  
Fine Structure ◽  
Statistical Model ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Contact Maps ◽  
Genome Wide ◽  
A Genome ◽  
Capture Method ◽  
Chromosome Maps

A statistical model describing a fine structure of the intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi–C) is proposed.

scholarly journals capC-MAP: software for analysis of Capture-C data

2019 ◽  
Vol 35 (22) ◽  
pp. 4773-4775 ◽  
Author(s):  
Adam Buckle ◽  
Nick Gilbert ◽  
Davide Marenduzzo ◽  
Chris A Brackley
Keyword(s):  
Software Package ◽  
Experimental Methods ◽  
Ease Of Use ◽  
Supplementary Information ◽  
Command Line ◽  
Supplementary Data ◽  
Chromosome Conformation ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Genomic Locations

Abstract Summary Capture-C is a member of the chromosome-conformation-capture family of experimental methods which probes the 3D organization of chromosomes within the cell nucleus. It provides high-resolution information on the genome-wide chromatin interactions from a set of ‘target’ genomic locations, and is growing in popularity as a tool for improving our understanding of cis-regulation and gene function. Yet, analysis of the data is complicated, and to date there has been no dedicated or easy-to-use software to automate the process. We present capC-MAP, a software package for the analysis of Capture-C data. Availability and implementation Implemented with both ease of use and flexibility in mind, capC-MAP is a suit of programs written in C++ and Python, where each program can be run separately, or an entire analysis can be performed with a single command line. It is available under an open-source licence at https://github.com/cbrackley/capC-MAP, as well as via the conda package manager, and should run on any standard Unix-style system. Supplementary information Supplementary data are available at Bioinformatics online.

Chromosome Conformation Capture on Chip (4C): Data Processing

2016 ◽  
pp. 243-261
Author(s):  
Benjamin Leblanc ◽  
Itys Comet ◽  
Frédéric Bantignies ◽  
Giacomo Cavalli
Keyword(s):  
Data Processing ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
On Chip

scholarly journals EVALUASI TINGKAT PENERIMAAN APLIKASI DATA POKOK PENDIDIKAN (DAPODIK) MENGGUNAKAN METODE TECHNOLOGY ACCEPTANCE MODEL (TAM) (Studi Kasus : Pemutakhiran Data PIP Menggunakan Aplikasi DAPODIK)

2019 ◽  
Vol 9 (2) ◽  
pp. 396-406
Author(s):  
Aryanto Aryanto
Keyword(s):  
Data Processing ◽  
Technology Acceptance ◽  
Technology Acceptance Model ◽  
Basic Education ◽  
Sampling Technique ◽  
Study Groups ◽  
Ease Of Use ◽  
Perceived Usefulness ◽  
Perceived Ease Of Use ◽  
Acceptance Model

ABSTRACT Smart Indonesia Program (PIP) is a direct cash assistance provided to underprivileged students with Smart Indonesia Card (KIP) as a marker / identity to ensure and ensure that children get the assistance of the Smart Indonesia Program. In order to monitor the distribution of KIP and to ensure that KIP has been accepted and can be utilized by the students, the Ministry of Education and Culture shall validate and update KIP recipient data through the Dapodik Application. Dapodik is an online and real time, based application that can be accessed and operated directly by all school operators in data entry, data processing, updating of PIP data, education personnel, students, periodic, sanitation, study groups and data of infrastructure school. This study aimed to evaluate the level of acceptance of basic education data applications (dapodik) using the method of Technology Acceptance Model (TAM). This study used 3 modified variables are Perceived Ease of Use (PEOU) and Perceived Usefulness (PU) as independent variable while Acceptance of IT as dependent variable. This study used simple random sampling as a sampling technique, with the number of respondents as many as 66 people operators. For data analysis techniques, this study used multiple regression techniques with descriptive quantitative research types, as well as data processing tools using SPSS 16.00 for windows software. The results showed that the benefit factor (Perceived Ease of Use) of 43.5%, factor amenity (Perceived Usefulness) of 36.8%. This proves that the more dominant benefit factor influences receipt of Dapodik application usage as PIP data updating application.   Key Words: Aplication of Dapodik, Perceived Ease of Use, Perceived Usefulness, Perceived Usefulness, Acceptance of IT, Technology Accaptance Mod

scholarly journals Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community

2021 ◽  
Vol 10 (17) ◽  
Author(s):  
Quentin Lamy-Besnier ◽  
Romain Koszul ◽  
Laurent Debarbieux ◽  
Martial Marbouty
Keyword(s):  
Murine Model ◽  
Bacterial Genome ◽  
Chromosome Conformation Capture ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
High Quality ◽  
Chromosome Conformation

ABSTRACT The Oligo-Mouse-Microbiota (OMM12) gnotobiotic murine model is an increasingly popular model in microbiota studies. However, following Illumina and PacBio sequencing, the genomes of the 12 strains could not be closed. Here, we used genomic chromosome conformation capture (Hi-C) data to reorganize, close, and improve the quality of these 12 genomes.

scholarly journals SisterC: A novel 3C-technique to detect chromatin interactions between and along sister chromatids

2020 ◽  
Author(s):  
Marlies E. Oomen ◽  
Adam K. Hedger ◽  
Jonathan K. Watts ◽  
Job Dekker
Keyword(s):  
Cell Cycle ◽  
Single Strand ◽  
Chromosome Conformation Capture ◽  
Brdu Incorporation ◽  
Chromosome Conformation ◽  
Strand Breaks ◽  
Chromatin Interactions ◽  
Sister Chromatids ◽  
Single Strand Breaks ◽  
Capture Techniques

Abstract Current chromosome conformation capture techniques are not able to distinguish sister chromatids. Here we describe the protocol of SisterC1: a novel Hi-C technique that leverages BrdU incorporation and UV/Hoechst-induced single strand breaks to identify interactions along and between sister chromatids. By synchronizing cells, BrdU is incorporated only on the newly replicated strand, which distinguishes the two sister chromatids2,3. This is followed by Hi-C4 of cells that can be arrested in different stages of the cell cycle, e.g. in mitosis. Before final amplification of the Hi-C library, strands containing BrdU are specifically depleted by UV/Hoechst treatment. SisterC libraries are then sequenced using 50bp paired end reads, followed by mapping using standard Hi-C processing tools. Interactions can then be assigned as inter- or intra-sister interactions based on read orientation.

scholarly journals A streamlined tethered chromosome conformation capture protocol

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Idan Gabdank ◽  
Sreejith Ramakrishnan ◽  
Anne M. Villeneuve ◽  
Andrew Z. Fire
Keyword(s):  
Chromosome Conformation Capture ◽  
Chromosome Conformation
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