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Modkit gives balanced map p-value in absence of replicates

4

Hi @ArtRand, I've noticed that `dmr` position will give a balanced map p-value in absence of replicates. Is this expected? The values look "real". For example: Thanks! In case I'm...

Ge0rges

Kolmogorov-Smirnov as a way of comparing methylomes

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Hi @ArtRand, I wanted to mention here a statistical test that might prove a useful contribution to modkit. In my study I have been trying to ask the question "How...

Ge0rges

Clarification on --model parameter in modkit open-chromatin predict

1

Hi, Thank you for developing such a powerful and user-friendly tool! I’m currently working on open chromatin prediction using modkit and had a question regarding the `--model` parameter in the...

DexinYang1998

Advice on Preserving Methylation Tags (ML/MN) When Switching from Minimap2 to BWA

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Hello dear community, I am studying epigenetics in cfDNA using ONT sequencing. I have reasons to suspect that minimap2 does not handle short reads

assafgrw

Inconsistency between inosine_m6A model and DRACH_m6A model

2

Hi, Currently I am suing [email protected] m6A_inosine and m6A_DRACH models to screen the cell line. I found that there were a lot of non-DRACH m6A sites when I used m6A_inosine...

wangziyuan66

Pileup - analyzing several mods and several motifs

3

Hi, Thanks for all the support with Modkit. I am using Dorado v1.0.0 and Modkit v0.5.0. Based on other issues I have looked at, I have started adding the --motif...

kylepalos

Modkit extract full 5hmCG + 5mCG > 1

2

Hello. I've been using modkit extract (now extract full) and adjust-mods for over a year now for methylation-based classification of human tumor samples, and I recently ran into a problem...

amurray411

Please clarify release files in v0.5.0

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Dear ONT Developers, Thank you for developing modkit. In the latest v0.5.0 release, there are multiple compiled binaries available and the file names are not descriptive enough to understand which...

SuhasSrinivasan

Understanding filtering, Nmod and Ncanonical

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Hello, I have a question about filtering the 10% lowest confidence modification calls, and how Nmod and Ncanonical values are obtained. If modkit (by default) first filters out the 10%...

imilenkovic

No results with the new RNA model

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Hello, I recently tried the new model released by dorado v1.0.0 for direct RNA, everthing works good except that I don't have any results with modkit dmr pair, which surprised...

rania-o