# Evaluation of Nanopore direct RNAseq data in Galaxy

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Direct RNA sequencing (DRS) using Oxford Nanopore technologies enables direct sensing of native RNA molecules. The RNA modification detection workflows for DRS data utilize the electrical deviations in the signal to identify RNA modifications directly in vivo by comparing the signal to unmodified RNA samples that are transcribed in vitro.

Up to now, two different works have tackled understanding the scope of SARS-CoV-2 genomic and sub-genomic RNAs using Nanopore DRS (Kim et al. and Taiaroa et al. ). Here, we provide workflows for the methylation analysis of SARS-CoV-2 within Galaxy framework in a scalable and reproducible fashion. In this way, we can provide a consistent analysis of the two available datasets. Thanks to the scalable nature of the Galaxy workflows, we will be able to consistenly process upcoming DRS data as well.

  1. Pre-processing of direct RNA data
  2. RNA methylation
description sample URL
Read mapping to viral genome Fr1,Fr2,Fr3,Korean workflow workflow run run
SARS-CoV-2: classify ONT reads by candidate junction regions Fr1,Fr2,Fr3,Korean workflow workflow run run
SARS-CoV-2: classify ONT reads by confirmed junction sites Fr1,Fr2,Fr3,Korean workflow workflow run run
Downsample reads to reduce coverage bias workflow workflow run run
Nanocompore sampcomp modification detection for three samples as one condition Fr-3, IVT workflow workflow run run
Tombo sample compare modification detection All workflow workflow run run
Map and downsample reads IVT workflow workflow run run
Variant analysis of isolates Fr1,Fr2,Fr3 history history view view
Construction of the combined human/SARS-CoV-2 reference genome Fr1,Fr2,Fr3 history history view view
Read mapping and sgRNA assignment Fr1 history history view view
Read mapping and sgRNA assignment Fr2 history history view view
Read mapping and sgRNA assignment Fr3 history history view view
Read mapping and sgRNA assignment Kr history history view view
Read mapping and sgRNA assignment Au history history view view
Read mapping and sgRNA assignment IVT history history view view
Nanopolish event alignment results All history history view view
Nanocompore modification results Fr1, Fr2, Fr3 history history view view
Tombo modification results All history history view view