Hi,
I have performed Illumina Hiseq metagenomic sequencing in ~200 samples of the upper respiratory system of patients and healthy volunteers. After removing human DNA, my samples contain ~2 Million microbial reads - the vast majority of them bacterial.
Nonetheless I would like to check if I can perform an analysis only in my viral reads. The problem is that when I am looking only at viral reads as these were assigned by Kaiju I have on average ~700 viral reads, with some samples containing even less than 100 reads. As expected, my rarefaction curves don't reach a plateau and whatever signal I have in my alpha and beta diversity plots from my bacterial reads is completely lost when I am looking at the virome of the two groups.
Based on that information can I claim that the viral reads of my dataset are very poor and should not be interrogated further? Is there another way to asses if the number of viral reads I have are enough for statistical analysis?
Thank you in advance for your help. Leonardos
