TRAPLINE : a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation

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dc.contributor.authorWolfien, Markusen_ZA
dc.contributor.authorRimmbach, Christianen_ZA
dc.contributor.authorSchmitz, Ulfen_ZA
dc.contributor.authorJung, Julia Jeannineen_ZA
dc.contributor.authorKrebs, Stefanen_ZA
dc.contributor.authorSteinhoff, Gustaven_ZA
dc.contributor.authorDavid, Roberten_ZA
dc.contributor.authorWolkenhauer, Olafen_ZA
dc.date.accessioned2017-07-25T12:04:12Z
dc.date.available2017-07-25T12:04:12Z
dc.date.issued2016
dc.descriptionCITATION: Wolfien, M., et al. 2016. TRAPLINE : a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. BMC Bioinformatics, 17:21, doi:10.1186/s12859-015-0873-9.
dc.descriptionThe original publication is available at https://bmcbioinformatics.biomedcentral.com
dc.description.abstractBackground: Technical advances in Next Generation Sequencing (NGS) provide a means to acquire deeper insights into cellular functions. The lack of standardized and automated methodologies poses a challenge for the analysis and interpretation of RNA sequencing data. We critically compare and evaluate state-of-the-art bioinformatics approaches and present a workflow that integrates the best performing data analysis, data evaluation and annotation methods in a Transparent, Reproducible and Automated PipeLINE (TRAPLINE) for RNA sequencing data processing (suitable for Illumina, SOLiD and Solexa). Results: Comparative transcriptomics analyses with TRAPLINE result in a set of differentially expressed genes, their corresponding protein-protein interactions, splice variants, promoter activity, predicted miRNA-target interactions and files for single nucleotide polymorphism (SNP) calling. The obtained results are combined into a single file for downstream analysis such as network construction. We demonstrate the value of the proposed pipeline by characterizing the transcriptome of our recently described stem cell derived antibiotic selected cardiac bodies ('aCaBs'). Conclusion: TRAPLINE supports NGS-based research by providing a workflow that requires no bioinformatics skills, decreases the processing time of the analysis and works in the cloud. The pipeline is implemented in the biomedical research platform Galaxy and is freely accessible via www.sbi.uni-rostock.de/RNAseqTRAPLINE or the specific Galaxy manual page (https://usegalaxy.org/u/mwolfien/p/trapline---manual).en_ZA
dc.description.urihttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0873-9
dc.description.versionPublisher's version
dc.format.extent11 pages
dc.identifier.citationWolfien, M., et al. 2016. TRAPLINE : a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. BMC Bioinformatics, 17:21, doi:10.1186/s12859-015-0873-9
dc.identifier.issn1752-0509 (online)
dc.identifier.otherdoi:10.1186/s12859-015-0873-9
dc.identifier.urihttp://hdl.handle.net/10019.1/102001
dc.language.isoen_ZAen_ZA
dc.publisherBioMed Central
dc.rights.holderAuthors retain copyright
dc.subjectData processingen_ZA
dc.subjectTransparent, Reproducible and Automated PipeLINE (TRAPLINE)en_ZA
dc.subjectTRAPLINEen_ZA
dc.subjectNucleotide sequenceen_ZA
dc.subjectRNA sequenceen_ZA
dc.titleTRAPLINE : a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotationen_ZA
dc.typeArticleen_ZA
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