Arthur Rand

Hello @melachl, Thanks for these numbers. I'm going to run some tests internally and compare. Just to confirm, you're using the SUP basecaller model and `[email protected]_6mA@v2` 6mA model, correct?

Hello @melachl, Sorry for the delay. I ran a test on some PCR and native DNA. I used `summary` to get an idea of the changes in 6mA in PCR...

Hello @Angelluigiguarnizo, Could you explain in detail what you mean by "gold methylations"? For DNA we have modified base models for 5mC/5hmC at any cytosine and 6mA at adenine. Meaning...

Hello @Angelluigiguarnizo, The adenine (6mA) model and cytosine (5hmC/5mC, 4mC/5mC) models are all "all-context" models. This means that you don't need to know the motif _a priori_, all As or...

Hello @angelluigi, You should not try and use the dna_R10 models with R9 data, the sensor is fundamentally different. There is a R9 flip-flop all-context model on [rerio](https://github.com/nanoporetech/rerio/tree/master/basecall_models#flip-flop-modified-base-models) that will...

Hello @OceaneMion, Sorry for the slow reply. Are you referring to the [table](https://nanoporetech.github.io/modkit/intro_extract.html#description-of-output-table) from `modkit extract`? As stated in the docs `mod_qual` is "probability of the base modification in the...

Hello @OceaneMion, The ouput of `pileup` is a count of how many reads called each modification (or canonical) at a given genome position. You get a "percent modification" from the...

@ArnavBharti, What makes your modBAM incompatible with `modkit pileup`? @Proy321 and @ArnavBharti, If you format your BED file so that the columns are the same as the bedMethyl [table](https://nanoporetech.github.io/modkit/intro_bedmethyl.html#bedmethyl-column-descriptions) used...

@PRIYANKA-22091995 You'll have to add or compute the missing values and remove the unnecessary ones. For example, you should know the modification code (or check the [SAM spec](https://samtools.github.io/hts-specs/SAMtags.pdf)). - Depth...

Hello @KevDonn, Here are 2 ways to aggregate 5hmC calls: (both ways require you to run `modkit pileup` first to generate a bedMethyl file) 1. Filter to positions only reporting...