Dear cn.mops crew,
I am trying cn.mops on a set of yeast genomes. Some issues:
- sometimes some strain lacks completely a certain chromosome, hence reads counts will be zero for that chromosome. Of course I can deal with this with preprocessing, but it would be very nice if cn.MOPS would not give an error but rather do something smarter
- I have a guess based on lab work on ploidy level of the samples. They vary from 4n to 2n. It would be very nice if this information could be used in the CNV counting instead of just giving a single ploidy level for all the samples.
Would you have recommendations on settings to use with this kind of samples? Especially the normalisation step is prone to fail with the whole chromosome losses I am seeing.