title: Identification and annotation of small RNA genes using ShortStack.
abstract: Highly parallel sequencing of cDNA derived from endogenous small RNAs (small RNA-seq) is a key method that has accelerated understanding of regulatory small RNAs in eukaryotes. Eukaryotic regulatory small RNAs, which include microRNAs (miRNAs), short interfering RNAs (siRNAs), and Piwi-associated RNAs (piRNAs), typically derive from the processing of longer precursor RNAs. Alignment of small RNA-seq data to a reference genome allows the inference of the longer precursor and thus the annotation of small RNA producing genes. ShortStack is a program that was developed to comprehensively analyze reference-aligned small RNA-seq data, and output detailed and useful annotations of the causal small RNA-producing genes. Here, we provide a step-by-step tutorial of ShortStack usage with the goal of introducing new users to the software and pointing out some common pitfalls.
authors.affiliation: Plant Biology Ph.D. Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; Department of Biology, Penn State University, University Park, PA 16802, USA.
authors.forename: Saima
authors.initials: S
authors.lastname: Shahid
authors.affiliation: Plant Biology Ph.D. Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; Department of Biology, Penn State University, University Park, PA 16802, USA. Electronic address: mja18@psu.edu.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Axtell
mesh_terms: D000818:Animals; D001483:Base Sequence; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D034741:RNA, Small Interfering / Q000235:genetics*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering
keywords: Bioinformatics; Genome annotation; High-throughput sequencing; Small RNA; microRNA; siRNA