I have a table which contains the number of different taxa in different samples from metagenomics data.
Sample seq_depth 16S counts taxa1 taxa2 taxa3 taxa4 1 55000 230 30 39 40 12 2 72000 300 23 53 20 64 3 137000 540 20 135 12 94 4 84000 250 48 37 102 74
I want to create a rarefaction curve based on that. What's the best way to do that? I have looked at the Qiime multiple_rarefaction.py) but the script doesn't take into consideration of the column B (Seq_depth) to create the rarefaction curve (we can ignore column C - 16S counts here). I was wondering when we use the input OTU table in Qiime do we provide sequencing depth info at all in a column or it just take Sample id and taxa columns?
In addition, if I want to create a new taxa counts table at an even sequencing depths (e.g. 50000) or at even 16S counts (e.g. 230) for all 4 samples. Is there a strategy to do that?