Arthur Rand

@PRIYANKA-22091995 Once you know which step is dropping the tags, I can advise you on how to use [modkit repair](https://nanoporetech.github.io/modkit/intro_repair.html) to _potentially_ replace the tags. Here are two `awk` commands...

Hello @jerry73204, thanks for pasting this! You're correct that `add_stream` might be more idiomatic. Do you know a way to add back pressure with that approach? For example imagine that...

Hello, Is it possible that you do not have BWA in your $PATH? If you un-comment lines 207 and 208 in runSignalAlign (https://github.com/ArtRand/signalAlign/blob/master/scripts/runSignalAlign.py#L207, then rebuild) it should give you the...

Hello John and Al, The output is `file_name\t#template_aligned_pairs(template_score)\tcomplement_aligned_pairs(complement_score)` The score is the average posterior probability of the aligned pairs, ignoring gaps.

Hello Jack, sorry about the slow reply. You can probably just add 1.23.0 at: https://github.com/ArtRand/signalAlign/blob/master/scripts/signalAlignLib.py#L261 If the HDF file structure is different, it should complain and you can probably track...

Hello @AzlanNI, As @marcus1487 mentioned, the two modeling approaches can lead to different results. Could you tell me how you're tabulating the number of positions "with a methylation value"? Is...

@AzlanNI > Would u suggest to change there the Thresholds as well ? We recommend letting `modkit` estimate the pass threshold automatically. If you are still confused by the results...

Hello @BioRB , Which methylation model are you using (e.g. 5mCG, 5hmCG, 6mA)?

Hello @BioRB and @melachl, Sorry for being slow to circle back. Could you tell me (again) which model(s) you're using and on what samples? We've tested the models on PCR...

@melachl, If you run `modkit summary $modbam --no-sampling --region chrM` on your modBAM, what level of 6mA is predicted in the two samples? My guess is the level of 6mA...