Arthur Rand

Hello @ywang285, If you don't have deep enough coverage to sample all of $\textbf{N}$ possible patterns (referring to the [documentation on the calculation](https://nanoporetech.github.io/modkit/intro_entropy.html#calculation-of-methylation-entropy)), the entropy calculation will be suppressed. For...

Hello @ywang285, I don't think you'll _need_ to sub-sample the amplified reads since they should have very low modification rates. If there is high native methylation entropy in a genomic...

Hello @saky7009, Are you using the `--segment` option, `--regions` or simply single-site analysis? In general `modkit` doesn't have any visualization _tools_ in it (yet). What we do, in general, is...

Hey @Ge0rges, It's planned, just need to do it. Thanks for showing interest in `entropy` I'll move it up the list.

@Ge0rges working on it. Next version of `entropy` will have some more functionality (including multi-base). Thanks for the poke.

Hello @Ge0rges here is a build that allows you to use multiple bases/motifs at once. For example: ```bash modkit entropy \ -s ./reads.bam \ -o ./output_dir \ --ref ${ref_fasta} \...

Hello @saky7009, Could you show me the what `$ head /gpfs2/scratch/mmolla/Longread_1/SP3/SP3_B/Withoutadjustmode/cpg_islands_ucsc_cleaned.bed` looks like and attach `/gpfs2/scratch/mmolla/Longread_1/SP3A_control_SP2A_Tumor/dmr.log`? Thanks.

@saky7009 could you send me the first few records from `gpfs2/scratch/mmolla/Longread_1/SP3/SP3_B/Withoutadjustmode/cpg_islands_ucsc_cleaned.bed`?

Hello @Yang990-sys, > May I ask if deleting all 0 rows will have an impact on it? For `modkit dmr pair` removing bedMethyl records with 0% modification will not yield...

Hello @galenptacek, This is a request I've gotten a couple times. I'll experiment with some algorithms and see if I can get it added in a future release.