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Hi I would like to know if all CpG are reported in the modkit pileup if we specify no-filtering ? Even those that are not methylated ?
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### Ask away!
Hi,
I have some bam files with modified base calls in any genomic context (5mC and 5hmC as opposed to 5mCG and 5hmCG). To analyse these, I'm trying to use the wf-human-variation, but I…
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Elevated mutation rates at CpG dinucleotides are one of the major contributors to mutation rate variation in mammals. These can't easily be simulated by `sim_mutations`, but there are probably reasona…
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# Stack trace
```
java.util.concurrent.ExecutionException: de.fraunhofer.aisec.cpg.frontends.TranslationException: Could not create type: translation context not available
at java.base/java.util…
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Hello,
I have some DNA methylation data, which I prepared using EM-Seq and got around 236 million paired-end reads after sequencing on the Illumina NextSeq platform. I have some concerns regarding …
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Would it be useful/advisable to have a link to the CPG somewhere near the top of this guide?
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Thanks for your work! I want to get an example of CPG, but when I tried to use your function:
```
cpg_file = process.joern_parse(joern_cli_dir, input_path, output_path, cpg_fname)
json_files = pro…
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When I use joern to scan C# projects, I encountered several issues:
1. For nodes of type 'fieldAccess', it cannot determine the type of the node. Additionally, there are occasional missing properti…
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https://batch.hail.populationgenomics.org.au/batches/443824/jobs/400
`ModuleNotFoundError: No module named 'cpg_utils.constants'`
in AnnotateVcf (SV)
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Hi.
I'm trying to do combine_CpG_sites with my 1359 samples.
However, the error message "Error! Cannot read input file 1021st sample" appears when receiving more than 1020 samples as input.
…