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Hello,
Thank you for developing this tool, it was very straightforward to install and run! I've run a rare methylation analysis by running `methbat profile` on 92 Revio HiFi datasets against the p…
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### Contact Details
jianan.luan@mrc-epid.cam.ac.uk
### Scripts
03d-non_genetic_methylation_pcs.sh
### What happened?
the script ./03d-non_genetic_methylation_pcs.sh failed with an error message "…
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Hi,
The following error occurs when I used f5c to call methylation and I wonder how this can be resolved. The script as f5c call-methylation -t 40 -r pass.fq.gz -b psss.bam -g genome.chr.fa --pore r…
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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 input for the `--segments` parame…
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Hi Arthur,
Thank you for this nice tool!!
I used modkit to call 5mC methylation at reference CpG sites! The command I used is below. (version mod_kit 0.3.2)
`modkit pileup --cpg --ref $ref -…
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### Contact Details
ks164@duke.edu
### Scripts
03b-methylation_adjustment1.sh
### What happened?
adjustment of methylation data at step 03b fails for my family data (MZ and DZ twins).
I run t…
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Hi，I used this command to extract methylation information：
modkit pileup ${mod_bam} ${bedmethyl_cpg} --cpg --ref ${ref} --no-filtering
However, I found that the CpG methylation information in the re…
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I am trying to extract read-level methylation information for 5mC and 5hmC.
I proceeded with the steps below, but I'm not confident if this is the correct approach, so I would like to ask for clarif…
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Running
```
python \
-m methylprep \
process \
-d /scratch/ucgd/lustre-labs/quinlan/data-shared/Neklason_MethylationEPIC_20241008/data \
--all
```
gives encouraging output i…
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Dear jts,
I want to find methylation in nanopore raw data. I have a computer that has 64GB RAM, 18TB HDD and AMD® Ryzen 9 7950x 16-core processor × 32.
The nanopore data were analysed as mentioned i…