LASCA: loop and significant contact annotation pipeline

Abstract Chromatin loops represent one of the major levels of hierarchical folding of the genome. Although the situation is evolving, current methods have various difficulties with the accurate mapping of loops even in mammalian Hi-C data, and most of them fail to identify chromatin loops in animal...

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Autores principales:	Artem V. Luzhin, Arkadiy K. Golov, Alexey A. Gavrilov, Artem K. Velichko, Sergey V. Ulianov, Sergey V. Razin, Omar L. Kantidze
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/69ccde0abe7745c6ae22aa14c46e9b5f
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id	oai:doaj.org-article:69ccde0abe7745c6ae22aa14c46e9b5f
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spelling	oai:doaj.org-article:69ccde0abe7745c6ae22aa14c46e9b5f2021-12-02T17:05:11ZLASCA: loop and significant contact annotation pipeline10.1038/s41598-021-85970-42045-2322https://doaj.org/article/69ccde0abe7745c6ae22aa14c46e9b5f2021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85970-4https://doaj.org/toc/2045-2322Abstract Chromatin loops represent one of the major levels of hierarchical folding of the genome. Although the situation is evolving, current methods have various difficulties with the accurate mapping of loops even in mammalian Hi-C data, and most of them fail to identify chromatin loops in animal species with substantially different genome architecture. This paper presents the loop and significant contact annotation (LASCA) pipeline, which uses Weibull distribution-based modeling to effectively identify loops and enhancer–promoter interactions in Hi-C data from evolutionarily distant species: from yeast and worms to mammals. Available at: https://github.com/ArtemLuzhin/LASCA_pipeline .Artem V. LuzhinArkadiy K. GolovAlexey A. GavrilovArtem K. VelichkoSergey V. UlianovSergey V. RazinOmar L. KantidzeNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Artem V. Luzhin Arkadiy K. Golov Alexey A. Gavrilov Artem K. Velichko Sergey V. Ulianov Sergey V. Razin Omar L. Kantidze LASCA: loop and significant contact annotation pipeline
description	Abstract Chromatin loops represent one of the major levels of hierarchical folding of the genome. Although the situation is evolving, current methods have various difficulties with the accurate mapping of loops even in mammalian Hi-C data, and most of them fail to identify chromatin loops in animal species with substantially different genome architecture. This paper presents the loop and significant contact annotation (LASCA) pipeline, which uses Weibull distribution-based modeling to effectively identify loops and enhancer–promoter interactions in Hi-C data from evolutionarily distant species: from yeast and worms to mammals. Available at: https://github.com/ArtemLuzhin/LASCA_pipeline .
format	article
author	Artem V. Luzhin Arkadiy K. Golov Alexey A. Gavrilov Artem K. Velichko Sergey V. Ulianov Sergey V. Razin Omar L. Kantidze
author_facet	Artem V. Luzhin Arkadiy K. Golov Alexey A. Gavrilov Artem K. Velichko Sergey V. Ulianov Sergey V. Razin Omar L. Kantidze
author_sort	Artem V. Luzhin
title	LASCA: loop and significant contact annotation pipeline
title_short	LASCA: loop and significant contact annotation pipeline
title_full	LASCA: loop and significant contact annotation pipeline
title_fullStr	LASCA: loop and significant contact annotation pipeline
title_full_unstemmed	LASCA: loop and significant contact annotation pipeline
title_sort	lasca: loop and significant contact annotation pipeline
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/69ccde0abe7745c6ae22aa14c46e9b5f
work_keys_str_mv	AT artemvluzhin lascaloopandsignificantcontactannotationpipeline AT arkadiykgolov lascaloopandsignificantcontactannotationpipeline AT alexeyagavrilov lascaloopandsignificantcontactannotationpipeline AT artemkvelichko lascaloopandsignificantcontactannotationpipeline AT sergeyvulianov lascaloopandsignificantcontactannotationpipeline AT sergeyvrazin lascaloopandsignificantcontactannotationpipeline AT omarlkantidze lascaloopandsignificantcontactannotationpipeline
_version_	1718381793716994048

LASCA: loop and significant contact annotation pipeline

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