Nanopore-based native RNA sequencing provides insights into prokaryotic transcription, operon structures, rRNA maturation and modifications

Felix Grünberger; Robert Knüppel; Michael Jüttner; Martin Fenk; Andreas Borst; Robert Reichelt; Winfried Hausner; Jörg Soppa; Sebastien Ferreira-Cerca; Dina Grohmann

(1) We used Tombo (Version 1.5, https://nanoporetech.github.io/tombo) to identify modified 267 bases based on a comparison to a theoretical distribution (de novo model) and based on the 268 comparison to a reference data set (sample-compare model) 47 . Briefly, for Fig. 6a reads mapping 269 to 16S rRNA were preprocessed, resquiggled and the raw signal plotted at a specific genomic 270 coordinate using the respective plotting command (tombo plot genome_locations). In addition, the 271 probability of modified bases was calculated using the detect_modification de_novo command. For 272 The copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2019.12.18.880849 doi: bioRxiv preprint created by sorting the reads mapping to the 16S rRNA based on the position of the read start 275 (before or after gene start), thereby dividing the data set in reads that belong to mature and 276 unprocessed 16S rRNAs. The two read sets were used as input for the sample-compare method. 277