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

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SamExploreR : Exploring reproducibility and robustness of RNA-seq results based on SAM files. / Stupnikov, Alexey; Tripathi, Shailesh; De Matos Simoes, Ricardo; McArt, Darragh; Salto-Tellez, Manuel; Glazko, Galina; Dehmer, Matthias; Emmert-Streib, Frank.

In: Bioinformatics, Vol. 32, No. 21, 01.11.2016, p. 3345-3347.

Research output: Contribution to journalArticleScientificpeer-review

Harvard

Stupnikov, A, Tripathi, S, De Matos Simoes, R, McArt, D, Salto-Tellez, M, Glazko, G, Dehmer, M & Emmert-Streib, F 2016, 'SamExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files', Bioinformatics, vol. 32, no. 21, pp. 3345-3347. https://doi.org/10.1093/bioinformatics/btw475

APA

Stupnikov, A., Tripathi, S., De Matos Simoes, R., McArt, D., Salto-Tellez, M., Glazko, G., ... Emmert-Streib, F. (2016). SamExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files. Bioinformatics, 32(21), 3345-3347. https://doi.org/10.1093/bioinformatics/btw475

Vancouver

Stupnikov A, Tripathi S, De Matos Simoes R, McArt D, Salto-Tellez M, Glazko G et al. SamExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files. Bioinformatics. 2016 Nov 1;32(21):3345-3347. https://doi.org/10.1093/bioinformatics/btw475

Author

Stupnikov, Alexey ; Tripathi, Shailesh ; De Matos Simoes, Ricardo ; McArt, Darragh ; Salto-Tellez, Manuel ; Glazko, Galina ; Dehmer, Matthias ; Emmert-Streib, Frank. / SamExploreR : Exploring reproducibility and robustness of RNA-seq results based on SAM files. In: Bioinformatics. 2016 ; Vol. 32, No. 21. pp. 3345-3347.

Bibtex - Download

@article{37e84bdb2e314d4fb06934a745d3c844,
title = "SamExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files",
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.",
author = "Alexey Stupnikov and Shailesh Tripathi and {De Matos Simoes}, Ricardo and Darragh McArt and Manuel Salto-Tellez and Galina Glazko and Matthias Dehmer and Frank Emmert-Streib",
year = "2016",
month = "11",
day = "1",
doi = "10.1093/bioinformatics/btw475",
language = "English",
volume = "32",
pages = "3345--3347",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "21",

}

RIS (suitable for import to EndNote) - Download

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.

U2 - 10.1093/bioinformatics/btw475

DO - 10.1093/bioinformatics/btw475

M3 - Article

VL - 32

SP - 3345

EP - 3347

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 21

ER -