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

The copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2019.12.18.880849 doi: bioRxiv preprint threshold of 1.5x (higher coverage upstream compared to downstream, see transcriptional unit 245 table in Supplementary Table 5) . 246 TSS were predicted by calculating the median start position of all reads that map to one gene and 247 cover the 5´ part of a CDS. To address the 3´ coverage bias and the underrepresentation of reads 248 that map to the 5´end and also for the 12 missing nucleotides at the TSS in general, all reads starting 249 at least 20 nt downstream of the annotated gene start were included. To not exclude too many 250 reads, the position of TTS were predicted similarly, by also including reads that have end positions 251 starting from 20 nt upstream of a gene end (TSS table in Supplementary Table 3, TTS table in 252 Supplementary Table 4) . 253