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LOGIQA: a database dedicated to long-range genome interactions quality assessment
posted on May 17, 2016
BMC Genomics 16 May 2016
Abstract
Proximity ligation-mediated methods are essential to study the impact of three-dimensional chromatin organization on gene programming. Albeit significant progress has been made in the development of computational tools that assess long-range chromatin interactions, next to nothing is known about the quality of the generated datasets. We have developed LOGIQA (www.ngs-qc.org/logiqa), a database hosting quality scores for long-range genome interaction assays, accessible through a user-friendly web-based environment. Currently, LOGIQA harbors QC scores for >900 datasets, which provides a global view of their relative quality and reveals the impact of genome size, coverage and other technical aspects. LOGIQA provides a user-friendly dataset query panel and a genome viewer to assess local genome-interaction maps at different resolution and quality-assessment conditions. LOGIQA is the first database hosting quality scores dedicated to long-range chromatin interaction assays, which in addition provides a platform for visualizing genome interactions made available by the scientific community.