Arthur Rand

Hello @Reziya, ```bash $ modkit extract full $bam $extract_output ``` Will extract 6mA calls if they are in your data. You can quickly check with `modkit modbam check-tags $bam --head...

Hello @DelphIONe, > Rep2 with modkit dmr gives new (different) positions compared to rep1 and these positions can't be true. Could you elaborate on what you mean by "positions can't...

@Ge0rges On my radar. I'll look asap - sorry about the delay.

For others looking at this issue. > Looking at this after posting it, could it be this is just because the coverage is too low? Does that track with the...

Hello @Wshengquan, Do you mean that you _never_ see the (-)-strand C calls or just not always? I usually see a pattern like this: ```text chr20 66405 66406 h 9...

Hello @Wshengquan, It is possible that you have reads covering the position on the negative strand but for one reason or another they don't have modification calls at that position....

Hello @meydaria, I agree this would be a convenient utility. All of the big features for the next release have been decided already - but I'll try and get this...

Hello @BrendanBeahan, Once again, your commands look fine. I reproduced the DMR table below to make it a little easier to read: | chrom | start | end | name...

Hello @BrendanBeahan, > In order to compare m6A-callers I was hoping to have some sort of continuous site-level confidence score, kind of like how m6Anet outputs site level modification probabilities...

Hello @baibhav-bioinfo, No this isn't the same. If you use `--modified-bases-threshold 0.92` any canonical probability >=0.92 will be elided (i.e. not explicitly recorded). If a base bas a canonical probability