modkit

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Modkit pileup issue with --include-bed

1

Hello all, we are trying to run modkit on an adaptive sampling run, and just started having issues with our normal pipeline after the most recent upodates to minknow. Generally,...

jcolicchio-soundag

modkit sample-probs with 2OmeACUG

2

Hi, @ArtRand I encountered some issues while using modkit sample-probs with 2OmeACUG. Here is my code: `${modkitDir}/modkit sample-probs ${bamfile}/input_merge_sup_m6A_pseU_m5C_inosine_2OmeACUG.mod.sorted.bam -t 40 --log-filepath ${bamfile}/input_merge_sup_2OmeA_sample_prob/input_merge_sup_2OmeA.sample_pob.log --percentiles 0.1,0.25,0.5,0.75,0.9 --out-dir ${bamfile}/input_merge_sup_2OmeA_sample_prob --hist --num-reads 20084...

kir1to455

modkit summary

2

Hello, If I want to achieve higher accuracy in _modkit summary_, is it appropriate to set the --mod-thresholds values based on the basecalling model in dorado for each modification type?...

hannan666666

pseudouridine (Ψ) modifications in RNA

1

Hi, I’m using modkit pileup to analyze pseudouridine (Ψ) modifications in RNA. However, when I visualize the results in IGV, I see that many called modification sites are not located...

gaoxiangcao

Modkit pileup extract multiple modifications

1

Hi, After basecalling, my modBAM contains multiple types of base modifications. I want to extract each modification type separately using modkit pileup, but I noticed that the --ignore option seems...

gaoxiangcao

6mA modification missing after modkit callmod

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Hi, The top track is the raw BAM file (grouped by read strand) after dorado base&modification calling. After I used the default` modkit call-mods ` (bottom), I found some of...

DexinYang1998

Question of DMR pair: output may be error?

4

I added some intermediate variable prints in your open-source code and found that the llr_ratio calculated by your beta_llk differs from the output of my Python implementation. The specific details...

WeiHea

PCA for modification distribution

1

Hi, Hope you are well. Is there a tool/strategy to make PCA plot for each modification showing the similarity between replicates. Does the distribution of m6A cluster between replicates?. Thanks...

kamaloxfordpathology

Question in “DMR model and scoring details”

1

When I implemented the single-site DMR score algorithm using the documentation at https://nanoporetech.github.io/modkit/dmr_scoring_details.html, the results I calculated did not match those from the official tool. ```pytthon import numpy as np...

WeiHea