v3v4 region parameters


I am following the 16S Microbial Analysis with mothur (extended).

I sequenced the v3v4 region using 341F and 806R primers.

The fragment length is 470 bp.

I just wasn’t to make sure I am entering the right parameters during my analysis since the training was done on the v4 region.

First Screen.seqs: I am using 480 bp for fragment length

Second Screen.seqs: “start” : 6352 and “end”: 25433 according to the mean values in the log file of the previous step.

Pre.cluster: Should I be using diff 2 or 4? Since it is 1 in every 100 bases and I have a 470 bp fragment…

Thank you!