Arthur Rand

Hello @sumudu-rangika, That's an interesting problem, thanks for explaining it. Out of curiosity, what is the effect size you're seeing in the promoter regions? Where does the score of the...

Hello @baibhav-bioinfo, If I'm understanding you correctly, the 1.6M m6A sites is _too many_ based on your understanding of the biology - correct? You could use a higher threshold for...

Hello @faulk-lab, I think you want `--filter-threshold` not `--filter-percentile`. However, this _might_ not do exactly what you want either. For a sanity check, could you show me what the `modkit...

Hello @faulk-lab, You want a command like this: ```bash modkit call-mods ${bam} - --filter-threshold A:1.0 --mod-threshold a:0.75 2> /dev/null | modkit extract - null --read-calls stdout --no-filtering 2>/dev/null | column...

@faulk-lab did you end up getting this sorted?

Hello @kamaloxfordpathology > I have aligned to the hg38 genome. When calculating modkit pileup, would reads that can align equally well to other positions add uncertainity to the RNA modification...

Hello @faulk-lab, Yeah I can look into adding that feature. It might be a few weeks since I'm slammed getting ready for our London Calling conference. I've also got some...

Hello @baibhav-bioinfo, > (1) But as i can see, the table contains no such row (site) which have 0 modification in one condition and something in other. The table have...

Hello @niradsp, These steps look fine. This problem can occur when the reference that you aligned to and the one you're using for pileup don't match. Are you sure that...

Hello @banskotan2, Modkit has a `dmr` module for pairwise comparisons. You can perform all pairwise comparisons with `modkit dmr multi` and look for trends or changes at specified regions, there...