Nanopore analysis on SARS-CoV-2 pseudouridylation

This directory contains scripts for the Nanopore analysis in "Discovering host protein interactions specific for SARS-CoV-2 RNA genome" by Giambruno et al. (doi: https://doi.org/10.1101/2022.07.18.499583). The analysis is performed on SARS-CoV-2 infected datasets from different cell line, with respect both to the viral SARS-CoV-2 genome or to the transcriptome NRCeq assembly (https://doi.org/10.1093/nar/gkac144).

How to run the analysis

Every submodule of the directory scripts contains a README.md file with the instructions to run the different parts of the analysis. Edit the general configuration file present in the general directory before running the analysis.

Content

• files : directory containing all the files necessary for the analysis
• scripts : directory containing all modules of the analysis and a general configuration file
  • general : directory containing a general configuration file to be set for the analysis
  • alignments : directory containing scripts to align reads to reference files
  • gRNA_mods_detection : directory containing scripts to detect modifications on genomic viral RNAs
  • sgRNAs_mods_detection : directory containing scripts to detect modifications on subgenomic viral RNAs