maybe it's a silly question, but I have very little experience with genome assembly, so I was hoping somebody would help me out. A colleague of mine has pointed out to certain number of N nucleotides in continuous parts of some genome assemblies (as in the middle of a chromosome). They are not present in human or mouse assemblies, but are seen quite often in other genomes.
Now what is confusing to me is those are not the hard-masked versions of the genomes - or at least so they said. Those are un-masked versions.
Could you have a certain number of Ns in an assembled scaffold? How could you know the number of Ns for sure if you never got the sequence?
Thank you for any input