Selected article for: "length read and read length"
Author: Felix Grünberger; Robert Knüppel; Michael Jüttner; Martin Fenk; Andreas Borst; Robert Reichelt; Winfried Hausner; Jörg Soppa; Sebastien Ferreira-Cerca; Dina Grohmann
Title: Nanopore-based native RNA sequencing provides insights into prokaryotic transcription, operon structures, rRNA maturation and modifications
  • Document date: 2019_12_19
    • ID: e5p4metz_7
    Snippet: Direct RNA-seq (-ax splice, -uf, -k14) and also with (1) -p set to 0.99, to return primary and 206 secondary mappings and (2) with --MD turned on, to include the MD tag for calculating mapping 207 identities. Alignment files were further converted to bam files, sorted and indexed using 208 SAMtools 41 . Strand-specific wig and bigwig files were finally created using bam2wig (Version 1.5, 209 https://github.com/MikeAxtell/bam2wig). To evaluate the.....
    Document: Direct RNA-seq (-ax splice, -uf, -k14) and also with (1) -p set to 0.99, to return primary and 206 secondary mappings and (2) with --MD turned on, to include the MD tag for calculating mapping 207 identities. Alignment files were further converted to bam files, sorted and indexed using 208 SAMtools 41 . Strand-specific wig and bigwig files were finally created using bam2wig (Version 1.5, 209 https://github.com/MikeAxtell/bam2wig). To evaluate the alignments, we first calculated the 210 aligned read length by adding the number of M and I characters in the CIGAR string 13 The definition of transcriptional units (TU) and our strategy to detect and annotate them was 232 based on a recent study that re-defined the bioinformatical search for transcriptional units (TU) 29 . 233

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