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chrisamiller / readDepth

R package for inferring copy number from read depth
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build annotations #10

Closed ChuanJ closed 2 years ago

ChuanJ commented 2 years ago

Hi, I want to build the annotation files by myself cause I am using hg38. Would you please tell me how to build them? Best,

chrisamiller commented 2 years ago

Unfortunately, the scripts for generating those annotations have been lost in one of the data migrations. The principles are straightforward, though, and the scripts used to generate annotations for copyCat (a more recent tool) should get you most of the way there: https://wustl.app.box.com/folder/141271265987?s=3950x2fdi5ra1tjxzk73l9hq5l0y7kzl

Best of luck!

ChuanJ commented 2 years ago

Thanks a lot! One quick question: is that possible to detect CNV from bisulfite sequencing data using these two tools?

chrisamiller commented 2 years ago

Yes - whole Genome bisulfite works just fine for CN detection

ChuanJ commented 2 years ago

And how about RRBS? Sorry, too many questions...

chrisamiller commented 2 years ago

No, the premise of these packages is that you're getting unbiased coverage across the genome and that depth can be converted to ploidy

ChuanJ commented 2 years ago

Okay, thanks for this important information!!!