Arthur Rand

Hello @Macdot3, This is a difficult question to answer in a very general case. A couple things you could try: 1. Run `modkit summary` and see what the methylation levels...

Hello @Macdot3, First off, I would use the `pass_frac` column to check on modification levels. This is the fraction of each modification call after applying the [thresholding](https://nanoporetech.github.io/modkit/filtering.html). A couple things...

Hello @Macdot3, As far as the number of reads in the `modkit summary` report, if the `--no-sampling` flag is passed all of the reads in the BAM will be used....

Hello @Macdot3, The two options, `--filter-threshold` and `--mod-threshold` are described in the [documentation](https://nanoporetech.github.io/modkit/filtering.html). The details of how the pass threshold is estimated is also in the [documentation](https://nanoporetech.github.io/modkit/filtering_numeric_details.html#filtering-base-modification-calls). In general, I...

Hello @Macdot3, Thanks for sending these results over. The 10% threshold in all of the samples is ~0.9, which is what I would expect. The minimum value you're seeing is...

Hello @Macdot3, The `mod_qual` is the probability of a specific modification (for example 5mC or 5hmC). Then the canonical probability is 1 - sum(P_mod). Please refer to section 1.7 of...

Hello @xiangpingyu, In general, you don't have to do anything to adjust the thresholds. The estimated threshold values in both of your samples seem to be about the same. If...

Hello @ArnavBharti, You must be loosing the MM/ML/MN tags somewhere along the way. Could you check that the records have these tags after each step? If you can tell me...

Hello @ArnavBharti, Could you check that the reads have the MM/ML/MN tags at the end of each step? I have a feeling that your basecalled FASTQ does not have them....

Hello @PRIYANKA-22091995 and @ArnavBharti, You need to run the basecalling such that you get and unaligned BAM file as output (not FASTQ output). I believe that the `--bam_out` flag will...