Phylotype and v3v4 region

[Funnyme186]

Hello @jennaj
Could you please advise regarding these two inquiries?

v3v4 region parameters

Hello, 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 usin…

OTUs clustering

Hello, I have a question regarding the otus clustering steps. I am not calculating error rates based on a mock community. So now, I should be using the Remove.lineage files instead of remove.groups in the Cluster.split, Make.shared and Classify.otu steps ? Is this correct? Is it the same for phylotype analysis? Thank you in advance, Best regards, Stephanie

Thank you in advance,
Best,
Stephanie