18S best region

Hi there everyone, I am a bit new in the data treatment from NGS, and since in Bacteria the V4 region is the optimal, as Pattrick Schloss states in several articles (and the workshop), I was thinking about 18S. Is there any “best region” for the 18 S? I have been thinking in 18Sv9 since v4 is pretty big and I fear it does not overlap well, but I do not know the resolution you can reach with 18S and Silva and if there are enough sequences represented. Also I dont know if i should adapt my reference alignment for fungi and protist separately.

Thanks in advance,

José Manjón-Cabeza

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