I am quite new to Metagenomics and how to statistically analyse my data.
I have run kraken2 to taxonomically profile my assembled metagenomics samples. I have three different disease state groups and I would like to see if there are any statistical differences between them. I decided to try to run metagenomeseq and/or phyloseq, however I am unsure of how to go from my kraken reports to inputting this into R.
I thought to create biom-tables with the program kraken-biom, but I am unsure if I should create one table per group or one table per sample.
Any information anyone has on Metagenome stats and using metagenomeseq/phyloseq I'd be grateful for your help!