Here we present the results obtained by probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess neuronal epitranscriptome plasticity. In this GitHub repository, you will find all the code used for the analysis/generation of figures. You can find all the files required to run the R script on Dropbox. We recommend downloading the files from Dropbox and substituting the paths to those on your local machine. Due to the size of the data we're hosting fast5 raw data for the Direct libraries on on NIH NCBI SRA under the accession number PRJNA1092333 and the IVT libraries under the accession number PRJNA947135, related to the panHumanIVT project.
The Figures.r R script can be executed in RStudio.
The CSV files containing the p-values analysis for psi detection has been generated using p-Mod ID.
The SNR files were generated using the SNR_marginal_likelihood.py script, executable in python.