GCC 2017

➔ Slides (doi: 10.7490/f1000research.1114423.1)

Authors
Mallory Freeberg, Biology Department, Johns Hopkins University (JHU)
James Taylor, Biology Department, Johns Hopkins University (JHU)


Abstract
Small RNAs are short, non-coding RNA molecules that play conserved roles in regulating gene expression across all metazoans. These ~20-50nt RNAs typically form sequence-specific RNA-RNA interactions with protein-coding mRNAs to regulate translation rates, promote RNA degradation, and maintain inheritence of epigenetic markers. To study small RNA populations on a global scale, second generation deep sequencing technologies are used to sequence and identify individual small RNAs among various cellular, genetic, and environmental contexts. Here, I will describe related Galaxy pipelines developed for the analysis of small RNA-seq datasets in the nematode Caenorhabditis elegans. These pipelines cover processing raw sequencing data, aligning reads to genome or small RNA references, classifying small RNA subcategories based on various features, and testing for differential expression of small RNAs. In addition to outlining the steps of small RNA-seq analyses, I will also discuss how the pipelines can be optimized for analyzing specific subclasses of small RNAs, which sometime require specialized parameters based on the underlying small RNA biology.