I have 3 fasta files of fungi genome assembly of 3 different assembler tools and in my fasta files there are some N characters wich represent the lot of Transposable elements in my genomes.
And i wanted to choose the best assembly beetween the 3 files compared to the N.
Is there a rule for N's that says that the one with the least N's is the best ?
There is a cutoff value for the N ?
I have also an other question : What is the way to identify centromer and telomer if they are masked because all repeted regions are N ?
Do i need to check about Repeat Maskers options?
Thanks for your answers.