2013
Methods
25 Jun 2013 Detection of non-coding RNA in Bacteria and Archaea using the DETR'PROK Galaxy pipeline.Claire Toffano-Nioche, Yufei Luo, Claire Kuchly, Claire Wallon, Delphine Steinbach, Matthias Zytnicki, Annick Jacq, Daniel Gautheret
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.
Keywords: NGS
Creation date: 19 Aug 2013
eZ PublishPublication supervisor: A-F. Adam-Blondon
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