Arthur Rand
Arthur Rand
@ArnavBharti I can get this to you next week.
Hello all, yes sorry for the delay.
Hello @Seongmin-Jang-1165, Sorry about the delay, and thanks for sending this data over. Taking a look at the proportions of m6A in your runs (in this case barcode 2): ...
Hello @Sepideh89, You do not need to re-run `pileup` if you have one `.bedmethyl` file for each condition you want to test. For example, if you want to compare two...
Hello @DexinYang1998, I'm going to guess that the light blue is 6mA and the red is 5mC - but correct me if I'm wrong. When you run `modkit call-mods` it...
Hello @DexinYang1998, In that case it makes sense that some of the calls will be removed (the lower confidence ones). It's hard to tell by eye, but it does look...
Hello @lance0499, really sorry about the delay getting back to you. To your questions: > Single-site analysis does not take a region file as an input. Do you have any...
Hello @shaperones It is a common misconception that the probabilities from `sample-probs` are the probability of modification. It's actually the probability of each modification _call_. For each A in a...
Hello @shaperones, You could use `modkit extract full` and calculate the median of the `mod_qual` column (optionally filtering on the `mod_code` column). If you're using a A/6mA model you could...
Hello @lbwfff The command you have here is fine. I'm currently working on a much faster version of the pileup algorithm that should help a lot. One thing you may...