This protocol is for preparing long reads for stranded mapping, as an intermediate step for additional protocols:Aligning strand-oriented sequences to a transcriptome for transcript / gene countingAligning strand-oriented sequences to a genome for confirmatory QCInput(s): demultiplexed fastq files (see protocol Demultiplexing Nanopore reads with LAST), adapter file (containing strand-sensitive adapter sequences)Output(s): oriented read files, as gzipped fastq files