Automated analysis of small RNA datasets with RAPID

Summary: Understanding the role of small RNA (sRNA) in diverse biological processes is of current interest and often approached through sRNA sequencing. However, analysis of these datasets is difficult due to the complexity of biological RNA processing pathways, which differ between species. Therefore, several different parameters should be analyzed, that were found to guide researchers, such as sRNA strand specificity, length distribution, and distribution of base modifications. We present RAPID, a generic sRNA analysis pipeline, which captures information inherent in the datasets and automatically produces numerous visualizations as user-friendly HTML reports, covering multiple categories required for sRNA analysis. RAPID also facilitates an automated comparison of multiple datasets, with different normalization techniques, and integrates differential expression analysis using DESeq2. Availability and Implementation: RAPID under MIT license at https://github.com/SchulzLab/RAPID or as a bioconda recipe https://bioconda.github.io/recipes/rapid/README.html.

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