2 votes

WGBS vs ONT, which one should I trust?

Methylation can be cell-specific, which makes it difficult to evaluate accuracy on a bulk-cell level (even within the same tissue). How can you tell that the differences you're seeing are due to ...
gringer's user avatar
  • 13.9k
2 votes

obtaining a fragment data file bed from bam

There's an example in the README (https://github.com/epifluidlab/cragr#example-datasets): For you information, below are steps from the BAM file to the fragment file: ...
jared_mamrot's user avatar
1 vote

Statistical approach to link DNA methylation with toxic element exposure and health outcome

Having given some thought to this, I'd still use machine learning. I would attempt to augment the negative controls however. Is there a suitable published data set? R program is caret but it high ...
M__'s user avatar
  • 12.1k
1 vote

Mendelian randomization

I understand linkage disequilibrium (LD) versus panmixia, which the technical term for Mendelian randomisation and for humans PLINK is a population package. The best outcome is a correlation between ...
M__'s user avatar
  • 12.1k
1 vote

WGBS vs ONT, which one should I trust?

I would assess directionality and accuracy of prediction by 1) WGBS predicting ONT and then 2) ONT predicting WGBS. Firstly, I would use deep learning (or machine learning) and train WGBS against ONT, ...
M__'s user avatar
  • 12.1k

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