Training Material For Small Rna-Seq Data Analysis (Galaxy Training Network Tutorial)

The data provided here are part of a Galaxy Training Network tutorial that analyzes small RNA-seq (sRNA-seq) data from a study published by Harrington et al. (DOI:10.1186/s12864-017-3692-8) to detect differential abundance of various classes of endogenous short interfering RNAs (esiRNAs). The goal of this study was to investigate "connections between differential retroTn and hp-derived esiRNA processing and cellular location, and to investigate the potential link between mRNA 3’ end cleavage and esiRNA biogenesis." To this end, sRNA-seq libraries were constructed from triplicate <em>Drosophila</em> tissue culture samples under conditions of either control RNAi or RNAi knockdown of a factor involved in mRNA 3’ end processing, <em>Symplekin</em>. This dataset (GEO Accession: GSE82128) consists of single-end, size-selected, non-rRNA-depleted sRNA-seq libraries. Because of the long processing time for the large original files, we have downsampled the original raw data files to include only reads that align to a subset of interesting transcript features including: (1) transposable elements, (2) <em>Drosophila</em> piRNA clusters, (3) <em>Symplekin</em>, and (4) genes encoding mass spectrometry-defined protein binding partners of <em>Symplekin</em> from Additional File 2 in the indicated paper by Harrington et al. More details on features 1 and 2 can be found here: https://github.com/bowhan/piPipes/blob/master/common/dm3/genomic_features (piRNA_Cluster, Trn). All features are from the <em>Drosophila</em> genome Apr. 2006 (BDGP R5/<em>dm3</em>) release.