samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files

Motivation: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (i) a cost efficient and (ii) an optimal experimental design leading to a compromise, e.g. in the sequencing depth of experiments.
Results: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes.
Availability and Implementation: samExploreR is available as an R package from Bioconductor.
Contact: [e-mail]
Supplementary information: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics - October 24, 2016 Category: Bioinformatics Authors: Stupnikov, A., Tripathi, S., de Matos Simoes, R., McArt, D., Salto-Tellez, M., Glazko, G., Dehmer, M., Emmert-Streib, F. Tags: GENE EXPRESSION Source Type: research