I am dealing with some problem, and i would be very happy if someone can help me here…
I have a large data set, i have already divided my data into different OTUs with 3% and 6% differences, i want to divide all of my sequences to new OTUs, the difference from each other in a much higher percentage, such as 15% or 20%. because of the large data set, the cluster split command didnt worked with cutoff higher then 0.09%, is there any possibility to set a specific cutoff, or in a range? such as 0.2-0.15? because calculating cutoffs from 0.2 until the minimum is not realistic
Thank you very much in advance!
Clustering at higher levels is unfortunately probably not realistic. Frequently people want these higher levels to say something about the number of phyla or classes in the dataset. If that’s your case, then I would just suggest using the classify.seqs and phylotype commands. That approach would probably be more meaningful if you are working with 16S rRNA gene sequence data.