2.1 Pre-processing
To run MeStudio, a pre-processing python script named ms_replacRhas been implemented to produce consistent formatting on the sequence identifiers from the genomic annotation, sequencer-produced modified base calls, and the genomic sequence file. To avoid possible inconsistencies at the sequence identifiers level (the “seqid” field) between FASTA and annotation files, we have implemented a quality check in this regard. More details are provided in the MeStudio manual on GitHub.