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GAMtools: an automated pipeline for analysis of Genome Architecture Mapping data

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Item Type:Preprint
Title:GAMtools: an automated pipeline for analysis of Genome Architecture Mapping data
Creators Name:Beagrie, R.A. and Schueler, M.
Abstract:Genome Architecture Mapping (GAM) is a recently developed method for mapping chromatin interactions genome-wide. GAM is based on sequencing genomic DNA extracted from thin cryosections of cell nuclei. As a new approach, GAM datasets require specialized analytical tools and approaches. Here we present GAMtools, a pipeline for analysing GAM datasets. GAMtools covers the automated mapping of raw next-generation sequencing data generated by GAM, detection of genomic regions present in each nuclear slice, calculation of quality control metrics, generation of inferred proximity matrices, plotting of heatmaps and detection of genomic features for which chromatin interactions are enriched/depleted.
Keywords:Chromosome Conformation, Genome Architecture Mapping, Chromatin Folding, Topological Domain, Nuclear Organisation
Publisher:Cold Spring Harbor Laboratory Press
Article Number:114710
Date:20 March 2017
Official Publication:https://doi.org/10.1101/114710

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