TADBD : a sensitive and fast method for detection of typologically associated domain boundaries
A topologically associated domain (TAD) is a self-interacting genomic block. Detection of TAD boundaries on Hi-C contact matrix is one of the most important issues in the analysis of 3D genome architecture at TAD level. Here, we present TAD boundary detection (TADBD), a sensitive and fast computatio...
| Publié dans: | BioTechniques. - 1993. - 69(2020), 1 vom: 01. Juli, Seite 376-383 |
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| Auteur principal: | |
| Autres auteurs: | , , , , |
| Format: | Article en ligne |
| Langue: | English |
| Publié: |
2020
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| Accès à la collection: | BioTechniques |
| Sujets: | Journal Article Research Support, Non-U.S. Gov't Hi-C haar-based algorithm topologically associated boundary detection Chromatin |
| Résumé: | A topologically associated domain (TAD) is a self-interacting genomic block. Detection of TAD boundaries on Hi-C contact matrix is one of the most important issues in the analysis of 3D genome architecture at TAD level. Here, we present TAD boundary detection (TADBD), a sensitive and fast computational method for detection of TAD boundaries on Hi-C contact matrix. This method implements a Haar-based algorithm by considering Haar diagonal template, acceleration via a compact integrogram, multi-scale aggregation at template size and statistical filtering. In most cases, comparison results from simulated and experimental data show that TADBD outperforms the other five methods. In addition, a new R package for TADBD is freely available online |
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| Description: | Date Completed 02.06.2021 Date Revised 02.06.2021 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1940-9818 |
| DOI: | 10.2144/btn-2019-0165 |