DNA copy number blacklist for excluding common unreliable regions

Question

[yura.grabovska]

Can anyone recommend some sources for reliable DNA copy number blacklists for excluding unreliable regions in the genome prior to copy number analysis?

[dthorbur]

Please include target species you are working on. These availability of these kinds of resources will be quite variable depending on how established your model system is. If you work on a non-model system, you might have to compile this list yourself, or filter results accordingly. For example, immune genes like MHC are particularly difficult to get an accurate copy number for without careful experimental design.