modkit
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nanoporetech
A bioinformatics tool for working with modified bases
Hi, I am running dmr pair for differential methylation scoring. My bed files are bgzipped and indexed. Here is the code used: ./modkit dmr pair -a CTRL.wf_mods.bedmethyl.gz -b DIFF.wf_mods.bedmethyl.gz -o...
Hi, i wanted to get the number (fraction) of reads in my samples that contain at least one methylated C. For that I tried using modkit summary on a sample...
First of all, thank you for this amazing tool! I am currently working on m⁶A analysis in a direct RNA sequencing (dRNA-seq) experiment. I basecalled my data using Dorado v1.0.0...
I used modkit to obtain a pileup.bed file. I want to count the 6mA modifications in the genome. Should I manually filter the data? For example, setting coverage > 5...
Sorry to bother you again, and thank you for your previous help. Below is my current understanding of the segmentation model — I’m not sure if it is fully correct,...
With the release of the latest model, inosine, m6A, and 2Ome can be called using the same model. At this point, it is difficult to use `modkit dmr` for one...
Hello, I was wondering whether mutated cytosines at CpG sites—such as those resulting in TG dinucleotides—are included in the calculation of beta values. Specifically, if a sequencing read contains a...
Dear developer, I am currently analyzing m6A-seq data generated from direct RNA sequencing and attempting to use modkit motif search for motif discovery. However, I have encountered some issues that...
This has been somewhat asked before but not fully... I want to know how I should interpret the cohen's h statistic. There isn't much to gather online beyond: h =...
Dear modkit team, we have been using modkit for a while and every time we need to select a different reference during the workflow as modkit does not allow for...
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A bioinformatics tool for working with modified bases