title: Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data.
abstract: Prokaryotic transcripts constitute almost always uninterrupted intervals when mapped back to the genome. Split reads, i.e., RNA-seq reads consisting of parts that only map to discontiguous loci, are thus disregarded in most analysis pipelines. There are, however, some well-known exceptions, in particular, tRNA splicing and circularized small RNAs in Archaea as well as self-splicing introns. Here, we reanalyze a series of published RNA-seq data sets, screening them specifically for non-contiguously mapping reads. We recover most of the known cases together with several novel archaeal ncRNAs associated with circularized products. In Eubacteria, only a handful of interesting candidates were obtained beyond a few previously described group I and group II introns. Most of the atypically mapping reads do not appear to correspond to well-defined, specifically processed products. Whether this diffuse background is, at least in part, an incidental by-product of prokaryotic RNA processing or whether it consists entirely of technical artifacts of reverse transcription or amplification remains unknown.
authors.affiliation: Bioinformatics Group; Department of Computer Science, and Interdisciplinary Center for Bioinformatics; University of Leipzig; Leipzig, Germany; Transcriptome Bioinformatics; LIFE - Leipzig Research Center for Civilization Diseases; University of Leipzig; Leipzig, Germany.
authors.forename: Gero
authors.initials: G
authors.lastname: Doose
authors.forename: Maria
authors.initials: M
authors.lastname: Alexis
authors.forename: Rebecca
authors.initials: R
authors.lastname: Kirsch
authors.forename: Sven
authors.initials: S
authors.lastname: Findeiß
authors.forename: David
authors.initials: D
authors.lastname: Langenberger
authors.forename: Rainer
authors.initials: R
authors.lastname: Machné
authors.forename: Mario
authors.initials: M
authors.lastname: Mörl
authors.forename: Steve
authors.initials: S
authors.lastname: Hoffmann
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D023281:Genomics / Q000379:methods; D058977:Molecular Sequence Annotation; D011387:Prokaryotic Cells / Q000378:metabolism*; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D012313:RNA
keywords: RNA-seq; circular sRNAs; self-splicing introns; split tRNAs