DEUS: an R package for accurate small RNA profiling based on differential expression of unique sequences.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 11 2019
01 11 2019
Historique:
received:
11
01
2019
revised:
05
06
2019
accepted:
18
06
2019
pubmed:
23
6
2019
medline:
25
6
2020
entrez:
23
6
2019
Statut:
ppublish
Résumé
Despite their fundamental role in various biological processes, the analysis of small RNA sequencing data remains a challenging task. Major obstacles arise when short RNA sequences map to multiple locations in the genome, align to regions that are not annotated or underwent post-transcriptional changes which hamper accurate mapping. In order to tackle these issues, we present a novel profiling strategy that circumvents the need for read mapping to a reference genome by utilizing the actual read sequences to determine expression intensities. After differential expression analysis of individual sequence counts, significant sequences are annotated against user defined feature databases and clustered by sequence similarity. This strategy enables a more comprehensive and concise representation of small RNA populations without any data loss or data distortion. Code and documentation of our R package at http://ibis.helmholtz-muenchen.de/deus/. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 31228198
pii: 5522007
doi: 10.1093/bioinformatics/btz495
pmc: PMC6853685
doi:
Substances chimiques
RNA
63231-63-0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4834-4836Informations de copyright
© The Author(s) 2019. Published by Oxford University Press.
Références
Bioinformatics. 2012 Dec 1;28(23):3150-2
pubmed: 23060610
Bioinformatics. 2006 Jul 1;22(13):1658-9
pubmed: 16731699
Nucleic Acids Res. 2015 Jul 1;43(W1):W467-73
pubmed: 26019179
Genome Biol. 2014;15(12):550
pubmed: 25516281
Nat Biotechnol. 2008 Apr;26(4):407-15
pubmed: 18392026
Nat Methods. 2016 Jul;13(7):577-80
pubmed: 27240256
Nat Protoc. 2013 Sep;8(9):1765-86
pubmed: 23975260
G3 (Bethesda). 2016 Jul 07;6(7):2103-11
pubmed: 27175019
Nucleic Acids Res. 2017 Dec 1;45(21):12140-12151
pubmed: 29069500
BMC Bioinformatics. 2015 Nov 04;16:354
pubmed: 26530785
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712