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

Aleksei Stupnikov, Shailesh Tripathi, Ricardo de Matos Simoes, Darragh McArt, Manuel Salto-Tellez, Galina Glazko, Matthias Dehmer, Frank Emmert-Streib

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

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 (a) a cost efficient and (b) 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: Availability: samExploreR is available as an R package from Bioconductor (after acceptance of the paper, download link: http://www.bio-complexity.com/samExploreR_1.0.0.tar.gz).


Original languageEnglish
Number of pages3
JournalBioinformatics
Early online date10 Jul 2016
DOIs
Publication statusPublished - 2016

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