samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files
Data(s) |
2016
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Resumo |
<p>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.</p><p>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.</p><p>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).</p><p><br/></p> |
Identificador | |
Idioma(s) |
eng |
Direitos |
info:eu-repo/semantics/closedAccess |
Fonte |
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 . DOI: 10.1093/bioinformatics/btw475 |
Tipo |
article |