Modification visualization

Generate mod.bam

Run SWARM_read_level.py with --modbam tag.

*Current implementation only supports single-threaded preprocessing which may result in slower prediction compared to default for models with Mini architecture (Ψ and m5C).

Process modbam

Use process_modbam.py to process modbam files for more informative visualisation of modifications.

Merge different modifications

process_modbam.py --inputs <INPUTS.tsv> -o <OUT>

Filter modification tags

Genome browsers visualise raw modification calls using colour scales that exaggerate the confidence in modification presence, having highly visible colours even for modification calls with probability under 0.5.

process_modbam.py -i <mod.bam> -o <OUT> -r <0.5> 

Filter coordinates

It is often useful to highlight modification trends in long reads only for a particular set of positions.

process_modbam.py -i <mod.bam> -o <OUT> --positions <BED>