Dear Bod,
THanks a lot for the reply and the link which I never notice before asking. It is really useful.
The samples that I am working with are human microbiome samples. However, I have a query here, if let's say I choose 12123 as the sampling depth, if I am right, this means that all my samples will be subsampled at 12123 reads and thus if I have a sample which has 100,000 reads, it will actually analyse only ~15% of the total read. It is worth to do so? And how do you know 6000 is sufficient? At the moment, I havent got a chance to come into contact with papers regarding this, do you have any to recommend?
Thanks.
Regards
Clara