This is Richa. I am analysing spatio-temporal data. I do not find Prochlorococcus sequences in my samples which are actually dominated by them (as confirmed by flow cytometry). Is this due to OTU picking method that mothur uses? What can I do about it? I am worried because I do find them in April samples when I analyse spatial data but while analysing seasonal data (in which the same April library is included as well), I do not find any prochlorococcus sequence at all. Why so ?
I am looking forward for help.
Thanks a lot…
Have you take a bona fide Prochlorococcus sequence, trimmed it to the length you are interested in and then tried to classify it? Some databases may still call it SAR11 and you may get the parent family if your region doesn’t have enough signal.
Hello Dr. Schloss,
Thanks for your reply.
NO, I have not taken any bona fide sequence of Prochlorococcus and tried to classify it, but I do see them in one data set. And while analyzing one library from the same data set with the other data set in which the probability of finding Prochlorococcus is more, I do not find even a single sequence of it.
I follow Miseq SOP. In case if prochlorococcus are being classsified as SAR11, could you please suggest me how I can solve this ?