NanoRMS2

NanoRMS2 is a pipeline for detection of DNA/RNA modifications. It requires two samples that differ in modification status, for example KO and WT.

The pipeline consists of three steps / modules:

• get_features: retrieve & store features in BAM file
• predict_mods: train ML models for modified bases, estimate per-position stoichiometry and much more...
• encode_mods: predict & encode per-read modification status in BAM file using ML models generated by predict step.

All these steps can be run separately or as a pipeline by executing nanoRMS2/run.

History

A simpler version of this work is NanoRMS. We recommend using NanoRMS2.

Requirements

You can find the software versions and requirements here.

Additional documentation

For more information, please visit full documentation.

Base-calling models

Modification-unaware basecalling models to be used with nanoRMS2 are stored in /data directory.

Citation

If you find this work useful, please cite:

Sonia Cruciani *, Anna Delgado-Tejedor *, Leszek P. Pryszcz ^#,*, Rebeca Medina, Laia Llovera and Eva Maria Novoa ^# De novo basecalling of m6A modifications at single-molecule and single-nucleotide resolution (under review)

-- The order of co-first authorship (* above) was determined by flipping the coin on 15 Jun 2023 at 14:53 CET @41.3848953,2.1939749.
In our opinion, such process summarises pretty well the randomness of success in science (and life in general!).