CHEUI (Methylation (CH3) Estimation Using Ionic current) is a software for the characterization of m6A and m5C RNA modifications from nanopore direct-RNA sequencing data. CHEUI can be used to detect m6A and m5C modifications at single read resolution and to identified modified sites and their stoichiometry in a transcriptome annotation in individual conditions, i.e. without the need of using a knock-out/knock-down or control sample (e.g. in-vitro trnscribed RNA). CHEUI also detects differential m6A or m5C between any two conditions.
CHEUI is open source and freely available from https://github.com/comprna/CHEUI under an Academic Public License (see copy of the license in this repository).
You can read more about CHEUI in this preprint
Identification of m6A and m5C RNA modifications at single-molecule resolution from Nanopore sequencing
P. Acera Mateos, A.J. Sethi, M. Guarnacci, A. Ravindran, A. Srivastava, J. Xu, K. Woodward,
W. Hamilton, J. Gao, L. M. Starrs, G. Burgio, R. Hayashi, V. Wickramasinghe, N. Dehorter,
T. Preiss, N. Shirokikh, E. Eyras. bioRxiv 2022.03.14.484124; doi.org/10.1101/2022.03.14.484124