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fanglab / nanodisco

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.
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Columns in nanodisco score output #40

Closed molleraj closed 1 year ago

molleraj commented 2 years ago

Hi - I have a quick question about the nanodisco score output. What does each output file column represent? This is not stated in the docs (https://nanodisco.readthedocs.io/en/latest/commands_details.html?highlight=coverage#score).

Any help would be greatly appreciated!

Thanks, Jon

touala commented 2 years ago

Hi @molleraj,

Thank you very much for the feedback. I've included a description in the documentation. In addition, I've briefly talked about the score in two other issues (#31 and #35) which could be informative.

If you have any additional questions, feel free to reach back to me,

Alan

molleraj commented 2 years ago

Hey Alan @touala

You are welcome! Thank you for doing this - much appreciated. I will let you know if I do, thanks again.

Jon @molleraj

molleraj commented 2 years ago

Hey Alan,

I checked your description and I do have one further question. How is coverage over a motif calculated for WGA and native read data?

Thanks, Jon

touala commented 1 year ago

Hi @molleraj,

This is obviously quite late to respond but for the sack of completeness, the coverage is computed from the number of map events on each genomic position. The code in found here.

Best,

Alan