Arthur Rand

Hello @gaoxiangcao, What is likely happening is there are single base mismatches (V>U) and these have pseU calls on them. You can omit thes bedMethyl records by using `--motif T...

Hello @e-manduchi, It looks like these bedMethyl records have `.` as the strand, meaning that Modkit `pileup` was run with `--combine-strands` or `--preset traditional`. What that means is you're summing...

@e-manduchi If you're willing to send over the BAM for this small window that would be helpful in debugging, thank you! email it to art.rand[at]nanoporetech.com please.

Hello @Ge0rges, Nice to hear from you. Seeing `balanced_map_pvalue` without replicates is expected. You probably already know this, but for anyone else reading, the `balanced_map_pvalue` works by calculating first the...

> So is it always correct to use the balanced p-value and balanced effect size then? I'm not sure I'd say it's "correct". If the balanced and "raw" MAP-based p-values...

Hello @cj528-cam, there is a description of the table schema [in the documentation](https://nanoporetech.github.io/modkit/intro_dmr.html#differential-methylation-output-format). You can also run `modkit dmr pair` with the `--header` flag to get a BED-compatible header line...

Hello @hannan666666, In general, we recommend using the estimated threshold values as a way to get the best accuracy. If you want to tune the behavior a little bit you...

Hello @gaoxiangcao, I would not recommend using `--ignore` as a way to select bedMethyl records. If you want to select records by their modification code I would use something like...

Hello @reshu23, CRAM format should work for `pileup` but is not currently supported in `entropy`. I can get to adding this capability.

Hello @reshu23 sorry I missed this comment from earlier. I haven't tested entropy with CRAM input, so I can't speak to the performance regression you're observing. Is there a way...