dorado and modkit for m6A identification

Question

[baibhu1234]

hello everyone, i am trying to run Dorado for m6A site identification

time   dorado   basecaller   rna004_130bps_hac\@v5.1.0    /pod5/   --modified-bases-models rna004_130bps_hac\@v5.1.0_m6A_DRACH\@v1/   --device cuda:all   --reference   ref.fa   >  sample1.bam

it generated bam file for each of my replicate i did convert the bam to bed using "modkit pileup" now i want to all the downstream analysis for m6A modification (transcript/genome site level analysis).... such as getting the most confident sites and site ratio for each replicate

Then at last i would like to get the DMR analysis between condition based on 3 replicates each.

[GenoMax]

Check modkit dmr for differential analysis as shown here: https://github.com/nanoporetech/modkit/blob/master/book/src/advanced_usage.md

[baibhu1234]

Thankyou so much, i will look upto the link

Apologies for the repeated posts, actually i am quite new to the field. but i will restrain from making new posts unless its needed