modkit

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Using segmenting on differential methylation

4

Hello @ArtRand , I would like to compare the methylations of 2 conditions by regions and not by a specific position. In the `modkit dmr pair` what should be the...

Raya-Faigenbaum-Romm

Quality of life suggestion for motif bed

2

Hi @ArtRand Just an unimpactful quality of life suggestion. It would be nice to have a `--contig` option on `motif bed` to restrict to the passed contig. Just a small...

Ge0rges

Final CpG of read detection

3

When looking through my ONT reads, I noticed that reads that end with a CG seem to not have an MM or ML tag associated with them. Is this expected...

benjamin-bfeng

threshold modification in modkit pileup

1

Hello, Appreciation for developing such helpful program. I am working with DRS data and using "Dorado+modkit" for m6A modification analysis. I ran Dorado for modification basecalling, then used dorado aligner...

baibhav-bioinfo

Haplotagged CRAM and bedmethyl

4

Hello, I do have a haplotagged CRAM file, and phased outputs from the epi2melabs/wf-human-variation workflow, we have used --mod with --phase parameter. I have bedmethyl files for haplotypes 1, 2...

umranyaman

Feature Request: Add --partition-tag option to "modkit extract calls"

2

Currently, the ```--partition-tag``` option is available for the ```modkit pileup``` command, allowing users to partition output into multiple bedMethyl files based on tag-value pairs. It would be beneficial to have...

zaka-edd

Dorado for basecalling vs modification detection

2

Hello everyone, I am new to nanopore DRS dataset, and just figuring out the different file formats and tools. "Dorado basecaller" can be used to actual basecall sequence reads from...

baibhav-bioinfo

fetching sequence failed, FASTA read interval was out of bounds

1

I also met this problem, when I ran this comman, `modkit pileup --ref /mnt/raid/syl/5mc/05_20250122/5_remora/4_remora_inference/4mer.fasta --cpg --ignore h --combine-strands 4mer.infer.sort.bam 4mer.infer.bed ` ``` > fetching sequence failed, FASTA read interval was...

TKsh6

fetching sequence failed error message when running pileup

8

Here is my procedure. First I ran dorado basecaller, where I required all modifications to be called: ` dorado basecaller -v sup,inosine_m6A,pseU,m5C --min-qscore 9 --emit-moves -b 64 --mm2-opts {params} --estimate-poly-a...

niradsp

I have some questions regarding the bed methyl file, would you help?

1

# Q1: Would you explain why there is difference? I have bed methyl file for cytosine modification, what I have understood for each modified site, it measures the frequency of...

ralanany