Detection of non-coding RNA in bacteria and archaea using the DETR-PROK Galaxy pipeline

RNA-seq experiments are now routinely used for the large scale sequencing of transcripts. In bacteria or archaea, such deep sequencing experiments typically produce 10-50 million fragments that cover most of the genome, including intergenic regions. In this context, the precise delineation of the no...

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Bibliographic Details
Published in:Methods (San Diego, Calif.) Calif.), 2013-09, Vol.63 (1), p.60-65
Main Authors: Toffano-Nioche, Claire, Luo, Yufei, Kuchly, Claire, Wallon, Claire, Steinbach, Delphine, Zytnicki, Matthias, Jacq, Annick, Gautheret, Daniel
Format: Article
Language:English
Subjects:
Archaea
Escherichia coli
Vibrio splendidus
Online Access:Get full text
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Summary:RNA-seq experiments are now routinely used for the large scale sequencing of transcripts. In bacteria or archaea, such deep sequencing experiments typically produce 10-50 million fragments that cover most of the genome, including intergenic regions. In this context, the precise delineation of the non-coding elements is challenging. Non-coding elements include untranslated regions (UTRs) of mRNAs, independent small RNA genes (sRNAs) and transcripts produced from the antisense strand of genes (asRNA). Here we present a computational pipeline (DETR-PROK: detection of ncRNAs in prokaryotes) based on the Galaxy framework that takes as input a mapping of deep sequencing reads and performs successive steps of clustering, comparison with existing annotation and identification of transcribed non-coding fragments classified into putative 5' UTRs, sRNAs and asRNAs. We provide a step-by-step description of the protocol using real-life example data sets from Vibrio splendidus and Escherichia coli.
ISSN:1046-2023
DOI:10.1016/j.ymeth.2013.06.003