Capture-seq protocol and TE-reX pipeline guidelines for detection of recombination of repeat elements in short- and long-DNA reads libraries

Recombination of repeat elements is an important source of genomic variation in human tissues. Here, we describe steps to prepare libraries enriched for repeat elements starting from the genomic DNA of any species. We also detail the computational post-processing of the TE-reX pipeline output to gen...

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Autores principales: Pascarella, Giovanni, Straniero, Letizia, Frith, Martin, Carninci, Piero
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9860146/
http://dx.doi.org/10.1016/j.xpro.2022.102027
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author Pascarella, Giovanni
Straniero, Letizia
Frith, Martin
Carninci, Piero
author_facet Pascarella, Giovanni
Straniero, Letizia
Frith, Martin
Carninci, Piero
author_sort Pascarella, Giovanni
collection PubMed
description Recombination of repeat elements is an important source of genomic variation in human tissues. Here, we describe steps to prepare libraries enriched for repeat elements starting from the genomic DNA of any species. We also detail the computational post-processing of the TE-reX pipeline output to generate datasets of putative somatic and polymorphic recombination events. For complete details on the use and execution of this protocol, please refer to Pascarella et al. (2022).
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spelling pubmed-98601462023-01-22 Capture-seq protocol and TE-reX pipeline guidelines for detection of recombination of repeat elements in short- and long-DNA reads libraries Pascarella, Giovanni Straniero, Letizia Frith, Martin Carninci, Piero STAR Protoc Protocol Recombination of repeat elements is an important source of genomic variation in human tissues. Here, we describe steps to prepare libraries enriched for repeat elements starting from the genomic DNA of any species. We also detail the computational post-processing of the TE-reX pipeline output to generate datasets of putative somatic and polymorphic recombination events. For complete details on the use and execution of this protocol, please refer to Pascarella et al. (2022). Elsevier 2023-01-14 /pmc/articles/PMC9860146/ http://dx.doi.org/10.1016/j.xpro.2022.102027 Text en © 2023 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Pascarella, Giovanni
Straniero, Letizia
Frith, Martin
Carninci, Piero
Capture-seq protocol and TE-reX pipeline guidelines for detection of recombination of repeat elements in short- and long-DNA reads libraries
title Capture-seq protocol and TE-reX pipeline guidelines for detection of recombination of repeat elements in short- and long-DNA reads libraries
title_full Capture-seq protocol and TE-reX pipeline guidelines for detection of recombination of repeat elements in short- and long-DNA reads libraries
title_fullStr Capture-seq protocol and TE-reX pipeline guidelines for detection of recombination of repeat elements in short- and long-DNA reads libraries
title_full_unstemmed Capture-seq protocol and TE-reX pipeline guidelines for detection of recombination of repeat elements in short- and long-DNA reads libraries
title_short Capture-seq protocol and TE-reX pipeline guidelines for detection of recombination of repeat elements in short- and long-DNA reads libraries
title_sort capture-seq protocol and te-rex pipeline guidelines for detection of recombination of repeat elements in short- and long-dna reads libraries
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9860146/
http://dx.doi.org/10.1016/j.xpro.2022.102027
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