Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments
- PMID: 28676233
- DOI: 10.1016/j.jbiotec.2017.06.1203
Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments
Abstract
RNA-Sequencing (RNA-Seq) has become a widely used approach to study quantitative and qualitative aspects of transcriptome data. The variety of RNA-Seq protocols, experimental study designs and the characteristic properties of the organisms under investigation greatly affect downstream and comparative analyses. In this review, we aim to explain the impact of structured pre-selection, classification and integration of best-performing tools within modularized data analysis workflows and ready-to-use computing infrastructures towards experimental data analyses. We highlight examples for workflows and use cases that are presented for pro-, eukaryotic and mixed dual RNA-Seq (meta-transcriptomics) experiments. In addition, we are summarizing the expertise of the laboratories participating in the project consortium "Structured Analysis and Integration of RNA-Seq experiments" (de.STAIR) and its integration with the Galaxy-workbench of the RNA Bioinformatics Center (RBC).
Keywords: Metatranscriptomics; Regulatory RNA; Transcriptomics; Workflow development.
Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.
Similar articles
-
Bioinformatics Pipeline for Transcriptome Sequencing Analysis.Methods Mol Biol. 2017;1468:201-19. doi: 10.1007/978-1-4939-4035-6_14. Methods Mol Biol. 2017. PMID: 27662878
-
A Guide for Designing and Analyzing RNA-Seq Data.Methods Mol Biol. 2018;1783:35-80. doi: 10.1007/978-1-4939-7834-2_3. Methods Mol Biol. 2018. PMID: 29767357
-
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.Nucleic Acids Res. 2017 Jul 3;45(W1):W560-W566. doi: 10.1093/nar/gkx409. Nucleic Acids Res. 2017. PMID: 28582575 Free PMC article.
-
Designing a transcriptome next-generation sequencing project for a nonmodel plant species.Am J Bot. 2012 Feb;99(2):257-66. doi: 10.3732/ajb.1100292. Epub 2012 Jan 19. Am J Bot. 2012. PMID: 22268224 Review.
-
Towards next generation CHO cell biology: Bioinformatics methods for RNA-Seq-based expression profiling.Biotechnol J. 2015 Jul;10(7):950-66. doi: 10.1002/biot.201500107. Epub 2015 Jun 9. Biotechnol J. 2015. PMID: 26058739 Review.
Cited by
-
A framework for the computational prediction and analysis of non-coding RNAs in microbial environmental populations and their experimental validation.ISME J. 2020 Aug;14(8):1955-1965. doi: 10.1038/s41396-020-0658-7. Epub 2020 Apr 28. ISME J. 2020. PMID: 32346084 Free PMC article.
-
Eimeria maxima-induced transcriptional changes in the cecal mucosa of broiler chickens.Parasit Vectors. 2019 Jun 4;12(1):285. doi: 10.1186/s13071-019-3534-4. Parasit Vectors. 2019. PMID: 31164143 Free PMC article.
-
Freiburg RNA tools: a central online resource for RNA-focused research and teaching.Nucleic Acids Res. 2018 Jul 2;46(W1):W25-W29. doi: 10.1093/nar/gky329. Nucleic Acids Res. 2018. PMID: 29788132 Free PMC article.
-
GLASSgo - Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence.Front Genet. 2018 Apr 17;9:124. doi: 10.3389/fgene.2018.00124. eCollection 2018. Front Genet. 2018. PMID: 29719549 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
