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

Bioinformatics. 2016 Nov 1;32(21):3345-3347. doi: 10.1093/bioinformatics/btw475. Epub 2016 Jul 10.


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: v@bio-complexity.comSupplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

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


  • RNA