SamExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files

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

Research output: Contribution to journalArticlepeer-review

9 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 (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.

Original languageEnglish
Pages (from-to)3345-3347
Number of pages3
JournalBioinformatics
Volume32
Issue number21
DOIs
Publication statusPublished - 1 Nov 2016
Externally publishedYes

Keywords

  • RNA/genetics
  • Reproducibility of Results
  • Research Design
  • Sequence Analysis, RNA
  • Software

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