LOGIQA: a database dedicated to long-range genome interactions quality assessment

BMC Genomics

Database

Pierre-Etienne Cholley¹  Marco-Antonio Mendoza-Parra¹  Matthias Blum¹  Hinrich Gronemeyer¹  Valeriya Malysheva¹ 

[1] Equipe Labellisée Ligue Contre le Cancer, Illkirch, France;Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France;Centre National de la Recherche Scientifique UMR 7104, Illkirch, France;Institut National de la Santé et de la Recherche Médicale U964, Illkirch, France;University of Strasbourg, Illkirch, France;

关键词: HiC;    Quality;    Chromatin architecture;   

DOI  :  10.1186/s12864-016-2642-1

 received in 2016-01-20, accepted in 2016-04-22,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundProximity 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.MethodWe 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.ResultsCurrently, 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.ConclusionsLOGIQA 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.

【 授权许可】

CC BY   
© Mendoza-Parra et al. 2016