Cargando…
sRNAnalyzer—a flexible and customizable small RNA sequencing data analysis pipeline
Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency o...
Autores principales: | , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716150/ https://www.ncbi.nlm.nih.gov/pubmed/29069500 http://dx.doi.org/10.1093/nar/gkx999 |
_version_ | 1783283887491776512 |
---|---|
author | Wu, Xiaogang Kim, Taek-Kyun Baxter, David Scherler, Kelsey Gordon, Aaron Fong, Olivia Etheridge, Alton Galas, David J. Wang, Kai |
author_facet | Wu, Xiaogang Kim, Taek-Kyun Baxter, David Scherler, Kelsey Gordon, Aaron Fong, Olivia Etheridge, Alton Galas, David J. Wang, Kai |
author_sort | Wu, Xiaogang |
collection | PubMed |
description | Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) measurement results across different platforms, miRNA mapping associated with miRNA sequence variation (isomiR) and RNA editing, and the origin of those unmapped reads after screening against all endogenous reference sequence databases. To address these issues, we built a comprehensive and customizable sRNA-Seq data analysis pipeline—sRNAnalyzer, which enables: (i) comprehensive miRNA profiling strategies to better handle isomiRs and summarization based on each nucleotide position to detect potential SNPs in miRNAs, (ii) different sequence mapping result assignment approaches to simulate results from microarray/qRT-PCR platforms and a local probabilistic model to assign mapping results to the most-likely IDs, (iii) comprehensive ribosomal RNA filtering for accurate mapping of exogenous RNAs and summarization based on taxonomy annotation. We evaluated our pipeline on both artificial samples (including synthetic miRNA and Escherichia coli cultures) and biological samples (human tissue and plasma). sRNAnalyzer is implemented in Perl and available at: http://srnanalyzer.systemsbiology.net/. |
format | Online Article Text |
id | pubmed-5716150 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-57161502017-12-08 sRNAnalyzer—a flexible and customizable small RNA sequencing data analysis pipeline Wu, Xiaogang Kim, Taek-Kyun Baxter, David Scherler, Kelsey Gordon, Aaron Fong, Olivia Etheridge, Alton Galas, David J. Wang, Kai Nucleic Acids Res Computational Biology Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) measurement results across different platforms, miRNA mapping associated with miRNA sequence variation (isomiR) and RNA editing, and the origin of those unmapped reads after screening against all endogenous reference sequence databases. To address these issues, we built a comprehensive and customizable sRNA-Seq data analysis pipeline—sRNAnalyzer, which enables: (i) comprehensive miRNA profiling strategies to better handle isomiRs and summarization based on each nucleotide position to detect potential SNPs in miRNAs, (ii) different sequence mapping result assignment approaches to simulate results from microarray/qRT-PCR platforms and a local probabilistic model to assign mapping results to the most-likely IDs, (iii) comprehensive ribosomal RNA filtering for accurate mapping of exogenous RNAs and summarization based on taxonomy annotation. We evaluated our pipeline on both artificial samples (including synthetic miRNA and Escherichia coli cultures) and biological samples (human tissue and plasma). sRNAnalyzer is implemented in Perl and available at: http://srnanalyzer.systemsbiology.net/. Oxford University Press 2017-12-01 2017-10-24 /pmc/articles/PMC5716150/ /pubmed/29069500 http://dx.doi.org/10.1093/nar/gkx999 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Computational Biology Wu, Xiaogang Kim, Taek-Kyun Baxter, David Scherler, Kelsey Gordon, Aaron Fong, Olivia Etheridge, Alton Galas, David J. Wang, Kai sRNAnalyzer—a flexible and customizable small RNA sequencing data analysis pipeline |
title | sRNAnalyzer—a flexible and customizable small RNA sequencing data analysis pipeline |
title_full | sRNAnalyzer—a flexible and customizable small RNA sequencing data analysis pipeline |
title_fullStr | sRNAnalyzer—a flexible and customizable small RNA sequencing data analysis pipeline |
title_full_unstemmed | sRNAnalyzer—a flexible and customizable small RNA sequencing data analysis pipeline |
title_short | sRNAnalyzer—a flexible and customizable small RNA sequencing data analysis pipeline |
title_sort | srnanalyzer—a flexible and customizable small rna sequencing data analysis pipeline |
topic | Computational Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716150/ https://www.ncbi.nlm.nih.gov/pubmed/29069500 http://dx.doi.org/10.1093/nar/gkx999 |
work_keys_str_mv | AT wuxiaogang srnanalyzeraflexibleandcustomizablesmallrnasequencingdataanalysispipeline AT kimtaekkyun srnanalyzeraflexibleandcustomizablesmallrnasequencingdataanalysispipeline AT baxterdavid srnanalyzeraflexibleandcustomizablesmallrnasequencingdataanalysispipeline AT scherlerkelsey srnanalyzeraflexibleandcustomizablesmallrnasequencingdataanalysispipeline AT gordonaaron srnanalyzeraflexibleandcustomizablesmallrnasequencingdataanalysispipeline AT fongolivia srnanalyzeraflexibleandcustomizablesmallrnasequencingdataanalysispipeline AT etheridgealton srnanalyzeraflexibleandcustomizablesmallrnasequencingdataanalysispipeline AT galasdavidj srnanalyzeraflexibleandcustomizablesmallrnasequencingdataanalysispipeline AT wangkai srnanalyzeraflexibleandcustomizablesmallrnasequencingdataanalysispipeline |