Arthur Rand

Hello @sahuno, I apologize for the slow response, I've been OOO. I'm using IGV 2.17.4 and if I name by file with the extension `.bedmethyl` then IGV will show me...

Hello @flofloflo-cell, I ran a quick simulation, and it seems that the pattern you're seeing is expected. Here's how it works: ```math \displaylines{ \textbf{C} \sim \text{Pois}(100) \\ \textbf{M} \sim \text{Beta}(0.5,...

@flofloflo-cell, Do these plots have 6mA and 5mC(G) calls bedMethyl records combined? The percent modified distribution makes me think you're mostly looking at 6mA calls (obviously there will be many...

Hello @flofloflo-cell, Thanks for performing this analysis. What appears to be happening (as I'm sure you've also noticed by now) is there are positions where the model is less confident,...

Hello @ZhihanNUS, In version v0.4.4 I changed the maximum allowed coverage for the MAP-based p-value from 300 to 100. After some additional experiments, I decided that beyond coverage of 100...

Hello @ZhihanNUS, Sorry for being slow to get back, but this is actually an area that I've been thinking a lot about. > If I understand correctly, for my experiment...

Hello @Tang-pro, The tabix backend hasn't changed between those two versions. What's likely is that the previous version was actually just ignoring the error. Could you check send me the...

Ok, let me get you a build with a little more reporting and that will simply report and pass over these errors.

Hello @rania-o, > The first one is why does modkit report positions as modified when the fraction of modified base is 0 ? Modkit `pileup` will report all reference positions...

Hello @dasn588, > 1. whether a genomic loci can have both 5mC and 5hmC methylation call From what you've shown here there are 8 reads with passing modification calls, 1...