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PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data

The iCLIP and eCLIP techniques facilitate the detection of protein–RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLI...

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Detalles Bibliográficos
Autores principales: Krakau, Sabrina, Richard, Hugues, Marsico, Annalisa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5746957/
https://www.ncbi.nlm.nih.gov/pubmed/29284540
http://dx.doi.org/10.1186/s13059-017-1364-2
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author Krakau, Sabrina
Richard, Hugues
Marsico, Annalisa
author_facet Krakau, Sabrina
Richard, Hugues
Marsico, Annalisa
author_sort Krakau, Sabrina
collection PubMed
description The iCLIP and eCLIP techniques facilitate the detection of protein–RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP (https://github.com/skrakau/PureCLIP), a hidden Markov model based approach, which simultaneously performs peak-calling and individual crosslink site detection. It explicitly incorporates a non-specific background signal and, for the first time, non-specific sequence biases. On both simulated and real data, PureCLIP is more accurate in calling crosslink sites than other state-of-the-art methods and has a higher agreement across replicates. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-017-1364-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-57469572018-01-03 PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data Krakau, Sabrina Richard, Hugues Marsico, Annalisa Genome Biol Method The iCLIP and eCLIP techniques facilitate the detection of protein–RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP (https://github.com/skrakau/PureCLIP), a hidden Markov model based approach, which simultaneously performs peak-calling and individual crosslink site detection. It explicitly incorporates a non-specific background signal and, for the first time, non-specific sequence biases. On both simulated and real data, PureCLIP is more accurate in calling crosslink sites than other state-of-the-art methods and has a higher agreement across replicates. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-017-1364-2) contains supplementary material, which is available to authorized users. BioMed Central 2017-12-28 /pmc/articles/PMC5746957/ /pubmed/29284540 http://dx.doi.org/10.1186/s13059-017-1364-2 Text en © The Author(s) 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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.
spellingShingle Method
Krakau, Sabrina
Richard, Hugues
Marsico, Annalisa
PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data
title PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data
title_full PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data
title_fullStr PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data
title_full_unstemmed PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data
title_short PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data
title_sort pureclip: capturing target-specific protein–rna interaction footprints from single-nucleotide clip-seq data
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5746957/
https://www.ncbi.nlm.nih.gov/pubmed/29284540
http://dx.doi.org/10.1186/s13059-017-1364-2
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