Arthur Rand
Arthur Rand
Hello @ralanany, I think you can probably format the bedMethyl output this way. Do you know what the `statistic` column is? From a quick read of the nanomethviz docs, I...
Hello @SimonChen1997, This may happen when you have a few reads that have a mis-call at a position causing them to have a base modification call. You can suppress emitting...
Hello @SimonChen1997, Yes the `--motif` argument will work for bacterial genomes. (You may also be interested in `modkit motif search`). You can use a single base "motif" to narrow to...
@SimonChen1997 great, happy to help.
Hello @Tesdhi, One way to check is to run ```bash modkit modbam check-tags --ignore-index --num-reads 100 ``` This is essentially the first 100 reads, it will report how many reads...
Hello @HenrydMl, Could you send me the `modkit pileup` command you're using as well as the calculated pass threshold that it reports (or the debug log)? You might want to...
I agree. Also allowing .gz references is probably a good idea.
Hello @Tang-pro, > Why is the number of a inconsistent? I'm assuming these counts are total passing modification calls, correct? My guess is that when you use `--ignore 17596` that...
> When performing modkit dmr analysis, if I only want to compare m6A, shouldn't I use --ignore 17596 to exclude other modifications? Yes, you can do that.
Hello @Yang990-sys, Thanks for finding this. I think `modkit dmr` should make the folder if it doesn't exist to align it's behavior with the rest of the commands. I'll make...