UROPA: a tool for Universal RObust Peak Annotation

Abstract The annotation of genomic ranges of interest represents a recurring task for bioinformatics analyses. These ranges can originate from various sources, including peaks called for transcription factor binding sites (TFBS) or histone modification ChIP-seq experiments, chromatin structure a...

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Autores principales:	Maria Kondili, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Mario Looso
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/07c5dac7268642de8a4a45160f168774
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spelling	oai:doaj.org-article:07c5dac7268642de8a4a45160f1687742021-12-02T16:06:52ZUROPA: a tool for Universal RObust Peak Annotation10.1038/s41598-017-02464-y2045-2322https://doaj.org/article/07c5dac7268642de8a4a45160f1687742017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02464-yhttps://doaj.org/toc/2045-2322Abstract The annotation of genomic ranges of interest represents a recurring task for bioinformatics analyses. These ranges can originate from various sources, including peaks called for transcription factor binding sites (TFBS) or histone modification ChIP-seq experiments, chromatin structure and accessibility experiments (such as ATAC-seq), but also from other types of predictions that result in genomic ranges. While peak annotation primarily driven by ChiP-seq was extensively explored, many approaches remain simplistic (“most closely located TSS”), rely on fixed pre-built references, or require complex scripting tasks on behalf of the user. An adaptable, fast, and universal tool, capable to annotate genomic ranges in the respective biological context is critically missing. UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for universal genomic range annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. These can be sensitive for feature type, distance, strand specificity, feature attributes (e.g. protein_coding) or anchor position relative to the feature. UROPA can incorporate reference annotation files (GTF) from different sources (Gencode, Ensembl, RefSeq), as well as custom reference annotation files. Statistics and plots transparently summarize the annotation process. UROPA is implemented in Python and R.Maria KondiliAnnika FustJens PreussnerCarsten KuenneThomas BraunMario LoosoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Maria Kondili Annika Fust Jens Preussner Carsten Kuenne Thomas Braun Mario Looso UROPA: a tool for Universal RObust Peak Annotation
description	Abstract The annotation of genomic ranges of interest represents a recurring task for bioinformatics analyses. These ranges can originate from various sources, including peaks called for transcription factor binding sites (TFBS) or histone modification ChIP-seq experiments, chromatin structure and accessibility experiments (such as ATAC-seq), but also from other types of predictions that result in genomic ranges. While peak annotation primarily driven by ChiP-seq was extensively explored, many approaches remain simplistic (“most closely located TSS”), rely on fixed pre-built references, or require complex scripting tasks on behalf of the user. An adaptable, fast, and universal tool, capable to annotate genomic ranges in the respective biological context is critically missing. UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for universal genomic range annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. These can be sensitive for feature type, distance, strand specificity, feature attributes (e.g. protein_coding) or anchor position relative to the feature. UROPA can incorporate reference annotation files (GTF) from different sources (Gencode, Ensembl, RefSeq), as well as custom reference annotation files. Statistics and plots transparently summarize the annotation process. UROPA is implemented in Python and R.
format	article
author	Maria Kondili Annika Fust Jens Preussner Carsten Kuenne Thomas Braun Mario Looso
author_facet	Maria Kondili Annika Fust Jens Preussner Carsten Kuenne Thomas Braun Mario Looso
author_sort	Maria Kondili
title	UROPA: a tool for Universal RObust Peak Annotation
title_short	UROPA: a tool for Universal RObust Peak Annotation
title_full	UROPA: a tool for Universal RObust Peak Annotation
title_fullStr	UROPA: a tool for Universal RObust Peak Annotation
title_full_unstemmed	UROPA: a tool for Universal RObust Peak Annotation
title_sort	uropa: a tool for universal robust peak annotation
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/07c5dac7268642de8a4a45160f168774
work_keys_str_mv	AT mariakondili uropaatoolforuniversalrobustpeakannotation AT annikafust uropaatoolforuniversalrobustpeakannotation AT jenspreussner uropaatoolforuniversalrobustpeakannotation AT carstenkuenne uropaatoolforuniversalrobustpeakannotation AT thomasbraun uropaatoolforuniversalrobustpeakannotation AT mariolooso uropaatoolforuniversalrobustpeakannotation
_version_	1718384821274673152

UROPA: a tool for Universal RObust Peak Annotation

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