- Oral presentation
- Open Access
Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data
BMC Bioinformatics volume 12, Article number: A7 (2011)
The current revolution in sequencing technologies allows us to obtain a much more detailed picture of transcriptomes via RNA-Sequencing. We have developed the first integrative online platform, oqtans, for quantitatively analyzing RNA-Seq experiments. Our approach of providing a self-contained machine image with the accessible, transparent Galaxy framework  minimizes the risk of using a third-party web service for data analysis. These services often disappear a few years after publication and render results irreproducible . With oqtans, bioinformatics becomes reproducible by providing analysis building blocks for a customized workflow of read mapping, transcript reconstruction and quantitation as well as differential expression analysis.
Oqtans includes a comprehensive machine-learning-powered toolsuite developed by the authors for NGS data analysis. PALMapper is a short-read mapper which efficiently computes both unspliced and spliced alignments at high accuracy by taking advantage of base quality information and computational splice site predictions . mTIM is a transcript reconstruction method, which exploits features derived from RNA-seq read alignments and from computational splice site predictions to infer the exon-intron structure of the corresponding transcripts. rQuant is based on quadratic programming. It simultaneously estimates biases inherent in library preparation, sequencing, and read mapping, and accurately determines the abundances of given transcripts . rDiff is a set of statistical test techniques that determine significant differences between two RNA-seq experiments to find differentially expressed regions with or without knowledge of transcripts.
We compare predictions to the published annotation at the intron and transcript levels. The performance of read aligners is shown in Fig. 1A from D. melanogaster data, and transcript segmentation tools in Fig. 1B, on C. elegans. Our tools, PALMapper and mTIM, outperform TopHat  and Cufflinks . Oqtans is available free and open-source, from http://oqtans.org as a virtual machine for cloud computing environments, and ready to use on our public compute cluster at http://bioweb.me/mlb-galaxy.
Goecks J, Nekrutenko A, Taylor J: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome biology 2010, 11(8):R86. 10.1186/gb-2010-11-8-r86
Schultheiss SJ, Münch MC, Andreeva GD, Rätsch G: Persistence and Availability of Web Services in Computational Biology. PLoS computational biology 2011, 6(9):e24914.
Jean G, Kahles A, Sreedharan VT, De Bona F, Ratsch G: RNA-Seq read alignments with PALMapper. In Current protocols in bioinformatics Edited by: Andreas D Baxevanis [et al]. 2010. Chapter 11:Unit 11 16 Chapter 11:Unit 11 16
Bohnert R, Ratsch G: rQuant.web: a tool for RNA-Seq-based transcript quantitation. Nucleic acids research 2010, 38(Web Server):W348–351. 10.1093/nar/gkq448
Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25(9):1105–1111. 10.1093/bioinformatics/btp120
Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L: Improving RNA-Seq expression estimates by correcting for fragment bias. Genome biology 2011, 12(3):R22. 10.1186/gb-2011-12-3-r22
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Schultheiss, S.J., Jean, G., Behr, J. et al. Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data. BMC Bioinformatics 12, A7 (2011). https://0-doi-org.brum.beds.ac.uk/10.1186/1471-2105-12-S11-A7
- Cloud Computing
- Virtual Machine
- Differential Expression Analysis
- Read Mapping
- Cloud Computing Environment