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Median modification probabilities with sample-probs

3

Hi, I'm using modkit 0.5.0 on ONT synthetic oligos dataset s3://ont-open-data/modbase-validation_2024.10/ I basecalled their 6mA pod5 from modbase-validation_2024.10/subset folder with [email protected]_6mA@v3 (--modified-bases-threshold 0), then I run: ``` modkit sample-probs \...

shaperones

Using Modkit with Transcriptome-Aligned BAM Files

1

Hi, I am working with modkit to analyze ONT direct RNA-seq data. I generated BAM files with modification tags aligned both to the genome and to the transcriptome. The reason...

lbwfff

100% skipped reads

12

Dear developer All of my reads were skipped after using modkit. Here are my steps. 1. The data were re-basecalled (using Dorado) in SUP mode $ data/dorado-0.9.1-linux-x64/bin/dorado basecaller --device cuda:all...

Hedi65

Clarification on Interpreting 5mC_5hmC Output from Modkit

5

Hello @ArtRand In this attached example, at position 813563–813564, I notice that in column 11 the value is reported as h:20.00, m:40.00. Does this indicate that the proportion of h...

Proy321

clarification on apparent discrepancy between snp.vcf and bedmethyl outputs

6

Hello, after running the epi2me human-variation workflow with --mod and --phased, in the snp.vcf file I see this location where the individual is homozygous alternate (C>T). The relevant vcf line...

e-manduchi

Differentially methylated CpG Islands using single-site analysis

3

Hi, I am using modkit DMR to find differentially methylated CpG islands between two samples (treated vs untreated). I have successfully identified DMRs using CpG islands as the "region" file,...

lance0499

[src/command_utils.rs::123][2025-06-25 22:29:14][DEBUG] estimated pass threshold 1 for primary sequence base C

10

I'm seeing something strange where for some of my samples the threshold is something crazy high like 1, instead of something more sensible. Is there anything I can do to...

billytcl

adjust-mods --cpg bug

1

Hi, Could there be a small bug here? The documentation of adjust-mods indicates that --cpg is a short-hand for --motif CG 0, however it seems that --cpg is not correctly...

tramelliwe

pileup-hemi

1

I want run hemi-methylation in 5mC context... modkit pileup-hemi -o ftr.bed --motif C 0 -r mtDNA.fasta -t 32 --no-filtering ftr.bam... i am getting error as Error! motif must be palindromic...

partha434

I cannot identify the DMR output file column names

2

Hello Everyone, I'd like to ask if you have got more number of columns that it listed in the table when use default thresholds? **For example, I put** dmr_result="location" echo...

cj528-cam