I’m a novice user of software like this and I’m trying to figure out why I’m getting such a low proportion of my reads assigned to Uniref90 / Metacyc pathways and also why when I regroup the genefamilies I end up with extremely few KEGG orthologs.
I started with DNA isolated from mouse stool, and had the sequences generated with a HiSeq (150bp single). I also filtered out reads from mice using kneaddata. After using Humann2, My Unmapped reads are somewhere around 88%. (I would love to post a portion of my data but I don’t know how to do that in-line with the text).
Any advice would be very helpful, thank you so much,