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. 2014 May 1;30(9):1300-1.
doi: 10.1093/bioinformatics/btt731. Epub 2014 Jan 11.

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis

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Free PMC article

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis

Vipin T Sreedharan et al. Bioinformatics. .
Free PMC article

Abstract

We present Oqtans, an open-source workbench for quantitative transcriptome analysis, that is integrated in Galaxy. Its distinguishing features include customizable computational workflows and a modular pipeline architecture that facilitates comparative assessment of tool and data quality. Oqtans integrates an assortment of machine learning-powered tools into Galaxy, which show superior or equal performance to state-of-the-art tools. Implemented tools comprise a complete transcriptome analysis workflow: short-read alignment, transcript identification/quantification and differential expression analysis. Oqtans and Galaxy facilitate persistent storage, data exchange and documentation of intermediate results and analysis workflows. We illustrate how Oqtans aids the interpretation of data from different experiments in easy to understand use cases. Users can easily create their own workflows and extend Oqtans by integrating specific tools. Oqtans is available as (i) a cloud machine image with a demo instance at cloud.oqtans.org, (ii) a public Galaxy instance at galaxy.cbio.mskcc.org, (iii) a git repository containing all installed software (oqtans.org/git); most of which is also available from (iv) the Galaxy Toolshed and (v) a share string to use along with Galaxy CloudMan.

Figures

Fig. 1.
Fig. 1.
Schematic workflows of the Oqtans use cases. (A) The general steps needed to perform the analysis. (B) Tools included in Oqtans used for differential expression and GO term enrichment analysis (use case 1). The same workflow in the Galaxy instance is shown in Supplementary Figure S1
Fig. 2.
Fig. 2.
(A) Performance comparison of two alignment programs integrated in Oqtans, evaluated on the data from the use case in terms of intron accuracy (see Supplementary Fig. S3 for details). Such comparative evaluations are made easy, since the replicability assertion of the Galaxy Oqtans setup ensures otherwise identical comparisons. (B) Performance comparison from Görnitz et al. (2011), where PALMapper and TopHat alignments are processed with the de novo transcript inference tools mTIM and Cufflinks, again demonstrating the value of Oqtans for comparisons of analysis tool

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