Fast Bootstrapping-Based Estimation of Confidence Intervals of Expression Levels and Differential Expression from RNA-Seq Data

Posted by: RNA-Seq Blog in Statistical Analysis June 15, 2017 2,821 Views

Researchers from Georgia State University present IsoEM2 and IsoDE2, new versions with enhanced features and faster runtime of the IsoEM and IsoDE packages for expression level estimation and differential expression. IsoEM2 estimates FPKM and TPM levels for genes and isoforms with confidence intervals through bootstrapping, while IsoDE2 performs differential expression (DE) analysis using the bootstrap samples generated by IsoEM2. Both tools are available with a command line interface as well as a graphical user interface through wrappers for the Galaxy platform.

Feature-based comparison of state-of-the-art RNA-Seq quantification tools

In the reference row, G stands for genome and T for transcriptome

Availability: The source code of this software suite is available at https://github.com/mandricigor/isoem2. The Galaxy wrappers are available at https://toolshed.g2.bx.psu.edu/view/saharlcc/isoem2_isode2/c6d2dbdf0a4d

Mandric I, Temate-Tiagueu Y, Shcheglova T, Al Seesi S, Zelikovsky A, Mandoiu II. (2017) Fast Bootstrapping-Based Estimation of Confidence Intervals of Expression Levels and Differential Expression from RNA-Seq Data. Bioinformatics [Epub ahead of print]. [abstract]