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Hi,
I'm wondering how the genetic variants on CpG sites are treated by aligned_bam_to_cpg_scores.
For example, when a diploid genome has a heterozygous SNP on a CpG site, how will the coverage and…
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### Version
1
### DataCap Applicant
Lucas Tang
### Project ID
5
### Data Owner Name
ENCODE Data Coordinating Center
### Data Owner Country/Region
United States
### Data Owner Industry
Life …
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NA counts are missing from results here (not in legacy)
```
curl 'http://localhost:8082/api/column-store/generic-assay-data-bin-counts/fetch?dataBinMethod=STATIC' \
-H 'Accept: application/json' …
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Hi,
There is a problem with representation of methylation: 2-color system for 5mC (as well as any other system) displays all called 5C the same color. It is either all blue, all red, or all pink, but…
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Hello,
I have added a simple code to perform feature selection in the Program function. To run this code, I need to add the MatrxStats package.
The code runs in my docker environment but fails in …
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Dear author,
I have a small question. How to use UMAP to analyze the differences in methylation levels of different kmer sequences, that is, Figure 1C in the article. I have calculated the met…
ZFF00 updated
1 month ago
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Hello,
the Debian Med team is maintaining nanopolish for official Debian. The recently released Debian 10 was the last Debian release featuring Python2 since this programming language is EOL. If …
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Before this change https://github.com/samtools/htslib/pull/1854 U was changed to N when read by samtools
Now it will be changed to T
However, I think it would be "better" if we could preserve U …
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As noted in point 1 here: https://github.com/broadinstitute/tensorqtl/issues/68
> there will be >400K CpG sites in the data compared to >20K genes. What would you suggest be a good cis_window for a…
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Hello,
I would like to explore extending this tool for barcoded short reads. I think it would be reasonably straight forward to capture the barcode with a pattern and store it in the metadata of th…