title: Bioinformatics Analysis of Small RNA Transcriptomes: The Detailed Workflow.
abstract: Next-generation sequencing became a method of choice for the investigation of small RNA transcriptomes in plants and animals. Although a technical side of sequencing itself is becoming routine, and experimental costs are affordable, data analysis still remains a challenge, especially for researchers with limited computational experience. Here, we present a detailed description of a computational workflow designed to take raw sequencing reads as input, to obtain small RNA predictions, and to detect the differentially expressed microRNAs as a result. The exact commands and pieces of code are provided and hopefully can be adapted and used by other researchers to facilitate the study of small RNA regulation.
authors: Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada, T1K 3M4. slava.ilyntskyy@uleth.ca.
authors: Slava
authors: S
authors: Ilnytskyy
authors: Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada.
authors: Andriy
authors: A
authors: Bilichak
mesh_terms: D001937:Brassica / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D015723:Gene Library; D023281:Genomics / Q000379:methods; D035683:MicroRNAs / Q000235:genetics; D011786:Quality Control; D034741:RNA, Small Interfering / Q000235:genetics; D058727:RNA, Small Untranslated / Q000235:genetics*; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome; D064878:Web Browser; D057188:Workflow
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering; D058727:RNA, Small Untranslated
keywords: Bioinformatics; DESeq; Differential expression; Illumina; Next-generation sequencing; Small RNA; microRNA