Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation

We present Mustache, a new method for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps. Mustache employs scale-space theory, a technical advance in computer vision, to detect blob-shaped objects in contact maps. Mustache is scalable to kilobase-resolution maps and reports...

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Autores principales: Roayaei Ardakany, Abbas, Gezer, Halil Tuvan, Lonardi, Stefano, Ay, Ferhat
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7528378/
https://www.ncbi.nlm.nih.gov/pubmed/32998764
http://dx.doi.org/10.1186/s13059-020-02167-0
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author Roayaei Ardakany, Abbas
Gezer, Halil Tuvan
Lonardi, Stefano
Ay, Ferhat
author_facet Roayaei Ardakany, Abbas
Gezer, Halil Tuvan
Lonardi, Stefano
Ay, Ferhat
author_sort Roayaei Ardakany, Abbas
collection PubMed
description We present Mustache, a new method for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps. Mustache employs scale-space theory, a technical advance in computer vision, to detect blob-shaped objects in contact maps. Mustache is scalable to kilobase-resolution maps and reports loops that are highly consistent between replicates and between Hi-C and Micro-C datasets. Compared to other loop callers, such as HiCCUPS and SIP, Mustache recovers a higher number of published ChIA-PET and HiChIP loops as well as loops linking promoters to regulatory elements. Overall, Mustache enables an efficient and comprehensive analysis of chromatin loops. Available at: https://github.com/ay-lab/mustache.
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spelling pubmed-75283782020-10-02 Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation Roayaei Ardakany, Abbas Gezer, Halil Tuvan Lonardi, Stefano Ay, Ferhat Genome Biol Method We present Mustache, a new method for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps. Mustache employs scale-space theory, a technical advance in computer vision, to detect blob-shaped objects in contact maps. Mustache is scalable to kilobase-resolution maps and reports loops that are highly consistent between replicates and between Hi-C and Micro-C datasets. Compared to other loop callers, such as HiCCUPS and SIP, Mustache recovers a higher number of published ChIA-PET and HiChIP loops as well as loops linking promoters to regulatory elements. Overall, Mustache enables an efficient and comprehensive analysis of chromatin loops. Available at: https://github.com/ay-lab/mustache. BioMed Central 2020-09-30 /pmc/articles/PMC7528378/ /pubmed/32998764 http://dx.doi.org/10.1186/s13059-020-02167-0 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Roayaei Ardakany, Abbas
Gezer, Halil Tuvan
Lonardi, Stefano
Ay, Ferhat
Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation
title Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation
title_full Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation
title_fullStr Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation
title_full_unstemmed Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation
title_short Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation
title_sort mustache: multi-scale detection of chromatin loops from hi-c and micro-c maps using scale-space representation
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7528378/
https://www.ncbi.nlm.nih.gov/pubmed/32998764
http://dx.doi.org/10.1186/s13059-020-02167-0
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