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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-03-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-85970-4 |
| _version_ | 1818722456307761152 |
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| 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 |
| collection | DOAJ |
| 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 . |
| first_indexed | 2024-12-17T20:54:55Z |
| format | Article |
| id | doaj.art-69ccde0abe7745c6ae22aa14c46e9b5f |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-17T20:54:55Z |
| publishDate | 2021-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-69ccde0abe7745c6ae22aa14c46e9b5f2022-12-21T21:32:54ZengNature PortfolioScientific Reports2045-23222021-03-011111910.1038/s41598-021-85970-4LASCA: loop and significant contact annotation pipelineArtem V. Luzhin0Arkadiy K. Golov1Alexey A. Gavrilov2Artem K. Velichko3Sergey V. Ulianov4Sergey V. Razin5Omar L. Kantidze6Institute of Gene Biology Russian Academy of ScienceInstitute of Gene Biology Russian Academy of ScienceInstitute of Gene Biology Russian Academy of ScienceInstitute of Gene Biology Russian Academy of ScienceInstitute of Gene Biology Russian Academy of ScienceInstitute of Gene Biology Russian Academy of ScienceInstitute of Gene Biology Russian Academy of ScienceAbstract 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 .https://doi.org/10.1038/s41598-021-85970-4 |
| spellingShingle | 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 Scientific Reports |
| title | 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_short | LASCA: loop and significant contact annotation pipeline |
| title_sort | lasca loop and significant contact annotation pipeline |
| url | https://doi.org/10.1038/s41598-021-85970-4 |
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