This document provides a general workflow and overview of the tools we have used to analyse Nanopore RNA-seq data in prokaryotes, including:
- Basecalling and demultiplexing of raw FAST5 reads using
guppy - Trimming of reads using
pychopper,cutadapt&samclip - Mapping of reads to the genome using
minimap2 - Gene abundance estimation using
salmon - Detection of transcript boundaries using
termseq_peaks - Read coverage analysis using
bedtools
You can also have a look at a protocol recently published in Methods in Molecular Biology outlining different steps of Nanopore RNA-seq analysis.