dorado and modkit for m6A identification
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.
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baibhu1234 •
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Check
modkit dmrfor differential analysis as shown here: https://github.com/nanoporetech/modkit/blob/master/book/src/advanced_usage.mdThankyou 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