Dear all,

Recently I saw a paper where cases and controls differed at the sequencing depth. I wonder if this indicates a systematic bias, or it may be due to biological variation. I will be more than happy to hear your opinion.

Other question is how these differences can influence the results of alpha-, beta-diversity and relative proportion comparisons.

In my opinion the richness could be influenced, but not Shannon and Simpson index, since they control for differences at the sequencing depth. The relative proportions of reads assigned to certain taxa also should not be influenced, since their purpose is to take into account the differences in sequencing depth. Again it will be nice to hear your opinion :)

Best,

Joanna