Differential methylation call using replicate samples

[demis001]

I want to call differential methylation regions (DMRs) between wild and captive groups. This is my first time using ONT sequencing data. I want to call the DMR without passing a pre-defined genomic region like CpG Island. Do you know any other tool that provides downstream analysis after Dorado modBam?

I tried this using modkit, it requires a pre-defind genomic region:

modkit dmr multi --min-valid-coverage 2 --ref ${REF} -s "$PILEUP_DIR/S192_merged_methylation.bed.gz" wild -s "$PILEUP_DIR/S442_merged_methylation.bed.gz" wild -s "$PILEUP_DIR/N150_mod_methylation.bed.gz" wild -s "$PILEUP_DIR/GM_merged_methylation.bed.gz" captive -s "$PILEUP_DIR/Mimi_merged_methylation.bed.gz" captive -s "$PILEUP_DIR/NZ_merged_methylation.bed.gz" captive --base C -o ${DMR_DIR} --prefix dmr_results -t ${THREADS} --log-filepath ${DMR_DIR}/dmr_call.log --force

The DMR has to be called using a sliding window, 3 min CpG, a window size of 300bp, etc. This is how we do it using the Illumina methylation route.

@demis001