Arthur Rand

Hello @blipinskiaima, Sorry about the delay. I will look into this.

Hello @blipinskiaima, Sorry about the delay. The `modkit update-tags` command isn't as well parallelized as some of the other commands, so it scans through the BAM and updates the MM/ML...

Hello @OceaneMion, > The MM tag encodes the positions of modified bases (e.g., methylated cytosines). Correct > The ML tag encodes, in 8 bits (0–255), the likelihood that the modification...

Hello @OceaneMion, > Do you think it would be useful to incorporate Nfail or Ndiff into the calculation? For example, instead of using: Nmod/Nvalid_cov do : Nmod/Nvalid_cov+Nfail+Ndiff and other parameters...

Hello @blipinskiaima, I've sent you email with this same message, but for folks reading this issue board I'll report the salient points here. One thing to check first is that...

@hannan666666 Sorry for the delay.

Hello @hannan666666 > The manual suggests that the segmentation model runs over all sufficiently-covered modified positions. However, in the output, all segment regions (Same or Different) only include positions that...

Hello @CrisDAndres, Sorry for the terribly long response time (new Modkit features are coming!). Nothing you're doing stands out as incorrect, but here are some considerations. You may want to...

Hello @hannan666666, There isn't an option to subset a bedMethyl by motif in `modkit stats`, but that's a good suggestion! Right now, the best way I can recommend is to...

Hello @EstabilloLL, > Is there any way to only look at 5mC modifications and disregard 5hmC completely in dmr pair? The best way to do this is to use `--ignore...