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Shians / NanoMethViz

https://shians.github.io/NanoMethViz/
Apache License 2.0
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DSS anda NanomethViz #29

Closed BeatrizFaustino closed 11 months ago

BeatrizFaustino commented 1 year ago

Hello, I would like to know how to use the files generated by DSS, within the NanoMethViz function.

I would be grateful for the help!

Shians commented 1 year ago

Which particular file do you have in mind? Did you use DSS on Nanopore long read data or BS-Seq data?

BeatrizFaustino commented 1 year ago

Hello, thanks for the reply! I used DSS for Nanopore long reads data. I have the callDMR.txt files as well as the nanopolish methylation calls! Can I view this data in NanoMethViz?

Shians commented 1 year ago

You may be able to use it to annotate regions using the anno_regions function in the plot_genes() function. It would be helpful if you could copy in the first few lines of callDMR.txt so I know what information it contains.

BeatrizFaustino commented 1 year ago

Thanks for the answer! Would I use the function for the callDMR.txt file generated by DSS?

The first two lines of the callDMR.txt file are:

chr start end length nCG meanMethy1 meanMethy2 diff.Methy areaStat NC_071502.1 34119813 34120183 371 24 0.191503162830865 0.0102306134088378 0.181272549422028 68.4118706848033

Thank you very much in advance for the help

Shians commented 1 year ago

Sorry I forgot to get back to this. The table you described should be able to be put into the anno_regions argument when using plot_gene() or plot_region() functions. This will cause a section to be highlighted in the line graph of average methylation profiles.