Hi,
I am trying to run the below script from QIIME installation but I can't figure out what should be the value of my parameters -m and -x.
Script - multiple_rarefactions.py -i otu_table.biom -m 10 -x 140 -s 10 -n 2 -o rarefied_otu_tables/ Here - -m and -x are from below link
From this link, I got to know that it is important to chose the rarefaction depths based on how many total sequences per sample you have. For example, it would not make sense to do rarefactions from 20 to 100 seqs/sample if I had a larger data set with an average of 5000 seqs/sample. If I did that, I would be throwing out a lot of my data and statistical power!
Still, it is unclear to me how to decide these parameters. What do they mean by "seqs" here. Does that mean average number of reads/ sample?
Please help.
