I have two batch of shotgun metagenomic sequences. Batch one has 20 samples with avg depth of 10 million sequences and batch 2 has 50 samples with avg depth of 25 million sequences. Will this difference in the sequencing depth cause a issue when I merge all the samples and do a diversity analysis (case vs control). Further is there a option like rarefying the sequences before diversity analysis like its there in qiime2?
Thank you