Arthur Rand

Hello @assafgrw, The short answer is no. If a read doesn't have a cytosine, the base modification model won't make a cytosine modification call on that read. You should see...

Hello @victorLLA, The `modkit summary` command works on the _read level_, so it's counting the number of base modification calls on each RNA molecule sequenced. On the other hand, `pileup`...

Hello @victorLLA, Could you tell me what the estimated pass threshold is for the two runs (w/ and w/o `--motif A 0`)? It should be near the top of the...

Hello @victorLLA, Thanks for sharing the logs. My initial throught was that the thresholds would be different when using `--motif` but they are the same for all of the primary...

Hello @Yang990-sys, Currently you cannot `--ignore` multiple modifications at once, but you can chain the commands to achieve what you want. ```bash $ modkit adjust-mods ${inbam} stdout --ignore a \...

@SuhasSrinivasan, Yes I can try to get this into the next release. One thing to keep in mind, however, is that `--ignore` is not _really_ the espoused method to discard...

Hello @Seongmin-Jang-1165, > When I run the modkit motif search command using the original bedmethyl file, the command executes without errors, but no motifs are extracted. I suspect this might...

Hello @ArnavBharti, > For 5mC 5hmC dataset I wanted to ask, effect_size, MAP-based p-value and score are affected by both m and h. Is there a way to compute these...

@ArnavBharti sorry about the delay > Will this form of analysis be in future release of modkit? > Or should I try to recreate the algorithm used for these columns...

Hello @eboileau! > I understand that a higher score could mean both changes in overall modification levels and changes in modification type, am I wrong? Correct. The "score" is the...