Masking (NNN...) in published sequence caused by low read # or repetitiveness... how to know which?

Question

[michael.nagle]

The NNN... can appear in place of nucleotides in cases where there is low # of reads as well as over repetitive regions when masking is enabled, right?

What does it take to figure which is the cause?

Answer 1

[WouterDeCoster]

I guess the easiest would be to compare (e.g. in UCSC genome browser) whether the region masked (e.g. by blatting the non-masked part) corresponds to an element in the repeatmasker track. (Unless you need to check more than a few parts and would like to automate this.)

Answer 2

[Michael]

Probably most N's in scaffolded assemblies are due to gaps between assembled contigs where contigs have been joined into the same scaffold but the intermittent sequence between them has not been determined.