TY - JOUR
T1 - SamExploreR
T2 - Exploring reproducibility and robustness of RNA-seq results based on SAM files
AU - Stupnikov, Alexey
AU - Tripathi, Shailesh
AU - De Matos Simoes, Ricardo
AU - McArt, Darragh
AU - Salto-Tellez, Manuel
AU - Glazko, Galina
AU - Dehmer, Matthias
AU - Emmert-Streib, Frank
PY - 2016/11/1
Y1 - 2016/11/1
N2 - 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.
AB - 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.
KW - RNA/genetics
KW - Reproducibility of Results
KW - Research Design
KW - Sequence Analysis, RNA
KW - Software
UR - http://www.scopus.com/inward/record.url?scp=84994666672&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btw475
DO - 10.1093/bioinformatics/btw475
M3 - Article
C2 - 27402900
AN - SCOPUS:84994666672
SN - 1367-4803
VL - 32
SP - 3345
EP - 3347
JO - Bioinformatics
JF - Bioinformatics
IS - 21
ER -