title: Detection and quantitative estimation of spurious double stranded DNA formation during reverse transcription in bacteria using tagRNA-seq.
abstract: Standard RNA-seq has a well know tendency to generate "ghost" antisense reads due to formation of spurious second strand cDNA in the sequencing process. We recently reported on a novel variant of RNA-seq coined "tagRNA-seq" introduced for the purpose of distinguishing primary from processed transcripts in bacteria. Incidentally, the additional information provided by the tags is also very suitable for detection of true anti-sense RNA transcripts and quantification of spurious antisense signals in a sample. We briefly explain how to perform such a detection and illustrate on previously published datasets.
authors.affiliation: a Department of Computational Biology ; KTH Royal Institute of Technology; AlbaNova University Center ; Stockholm , Sweden.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Innocenti
authors.affiliation: b INRA; UMR1319 Micalis; Domaine de Vilvert ; Jouy-en-Josas , France.|c AgroParisTech; UMR Micalis; Domaine de Vilvert ; Jouy-en-Josas , France.
authors.forename: Francis
authors.initials: F
authors.lastname: Repoila
authors.affiliation: a Department of Computational Biology ; KTH Royal Institute of Technology; AlbaNova University Center ; Stockholm , Sweden.|d Department of Information and Computer Science ; Aalto University ; Espoo , Finland.
authors.forename: Erik
authors.initials: E
authors.lastname: Aurell
mesh_terms: D001419:Bacteria / Q000235:genetics*; D004247:DNA / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D048348:Reverse Transcription; D017423:Sequence Analysis, RNA
chemical_list: D004247:DNA
keywords: DNA; antisense RNA; complementary; spurious second strand cDNA; tagRNA-seq; transcript discovery; transcriptome