Arthur Rand

Hello @Manoswini-02, If you only want bedmethyl rows with 5hmC records, you can filter the output through `awk`: ```bash $ modkit pileup ${mod_bam} stdout [options] | awk '$4=="h"' > 5hmC.bedmethyl...

Hello @BarbaraSlap, No corrections are applied, the output has a raw MAP-based p-value. Thanks for the reminder, I need to add this to the documentation. I've found that the Benjamini-Hochberg...

Hey @Ge0rges, I agree that `modkit dmr multi` should handle replicates the way that the other `dmr` commands do when you've annotated them like you have here. I can work...

Hello @Ge0rges, As of [Version 0.4.0](https://github.com/nanoporetech/modkit/releases/tag/v0.4.0) you can use multiple replicates in `dmr pair multi` by using the same name for samples to be combined. Using your example: ``` modkit...

Hello @lkwhite, Unfortunately how $P_{\text{canonical}}$ is calculated is buried in the [SAM specification](https://samtools.github.io/hts-specs/SAMtags.pdf) see page 9 under the `ML` tag specification. > Are these converted from Phred-based QUAL scores in...

Hello @MarioRinBarr, Sorry for the delayed response. Let me see if I can take on your questions one at a time. > When I get the table, which I attach...

Hello @MarioRinBarr, > So I would expect the Nvalid values to be very high and similar. But this does not happen: Nvalid is only 1, and looking at the assembly,...

@lkwhite No, if you pass `--filter-threshold 0.98` then all base modification predictions (modified _or_ canonical) must have a probability >= 0.98. So if you have just a single modification, using...

Hello @OceaneMion, Positions with $N_{\text{valid}}$ will not get bedMethyl records, so if you have set the `--no-filtering` flag, CpGs without any read coverage will not be reported, as [documented](https://nanoporetech.github.io/modkit/troubleshooting.html#cg-positions-are-missing-from-output-bedmethyl). One...

Hello @OceaneMion, > What I would like to know also is how to get a table with the number of potentially methylated site with 5hmC, then the one with 5mC,...