TBI-p-2013-7
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Titel:
Mapping the RNA-Seq Trash Bin: Unusual Transcripts in Prokaryotic Transcriptome Sequencing Data
Author(s):
Doose, Gero and Alexis, Maria and Kirsch, Rebecca and Findeiß, Sven and Langenberger, David and Machne, Rainer and Moerl, Mario and Hoffmann, Steve and Stadler, Peter F.
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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 artefacts of reverse transcription or amplification remains unknown.
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Last modified: 2008-10-22 12:23:11 fall