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Hi team,
It was seeing your poster at ISME. I wanted to follow up on my question with an issue to serve as a (hopefully useful) reminder. It would be cool to benchmark your motif finding with `modk…
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Hi,
It's my first time doing DNA methylation, I'm a little bit confused about the results from the pileup and summary.
1. Are the pileup results from the **pass_frac** in the summary? how do th…
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Hello there,
I just run modkit pileup on my freshly aligned RNA direct sample and after running it, the column "modified base code" is displaying 17802 for some rows ? By any chance would you know…
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Hi, @ArtRand
I encountered some issues while using modkit extract.
Here is my code:
`${modkitDir}/modkit extract ${bamfile}/input_merge_sup_m6A_pseU.mod.sorted.bam null --read-calls ${bamfile}/inp…
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Hey I recently am running modkit on/around some structural variant calls. I was interested in using `modkit extract` to extract the methylation status within each reads on and around SVs. However, wh…
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Hi, it is my first time to use Modkit to extract modified base signals but have some problems.
I use Dorado v0.7.1 to do SUP + modification calling (m6A,pseU).
I use minimap2 to align the unaligne…
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"Running C:/Program Files/Epic Games/UE_5.4/Engine/Build/BatchFiles/Build.bat -projectfiles -project="C:/Users/emmet/Downloads/PavlovVR-ModKit-5.1.1/PavlovVR-ModKit-5.1.1/Pavlov.uproject" -game -rock…
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Hi,
I am interested in context specific methylation events and I am seeing some strange association between the predicted percentage of modification and the coverage at a given site. I followed the…
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### Need
As a user, I want clear outputs. At the moment variant files are a mix of vcf and bcf, some indexed and some not, some compressed and some not.
### Suggested approach
Standardise output va…
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Hi,
I've been puzzled by the lack of calls/site for CHG and CHH methylation for a few days now. I called similar data with Megalodon and modbamtobed a year or two ago and got very different results…