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

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

SUBMITTER: Sreedharan VT 

PROVIDER: S-EPMC3998122 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature