Hi,
I am running a WGS dataset through humann3 and in 5 of the 5 first samples, I only detect E.coli. I don’t expect a lot of bacteria in these samples since it is blood samples, but I wonder why E.coli turns up in most samples? Something wrong with my annotations? I updated databases based following the tutorial.
Gene Family SRR3163377_Abundance-RPKs
UNMAPPED 192889548.0000000000
UniRef90_A0A329XME7 5588517.9572251709
UniRef90_A0A329XME7|g__Escherichia.s__Escherichia_coli 5588517.9572251709
UniRef90_UPI000BB85CB4 2435365.2982355496
UniRef90_UPI000BB85CB4|g__Escherichia.s__Escherichia_coli 2435365.2982355496
UniRef90_A0A1X3K551 2374320.5282771089
UniRef90_A0A1X3K551|g__Escherichia.s__Escherichia_coli 2374320.5282771089
UniRef90_A0A2I2ZPI1 1890437.5465917028
UniRef90_A0A2I2ZPI1|g__Escherichia.s__Escherichia_coli 1890437.5465917028
UniRef90_A0A2B3TG24 1570004.5673570558
UniRef90_A0A2B3TG24|g__Escherichia.s__Escherichia_coli 1570004.5673570558
UniRef90_A0A1X3K7C5 1564615.7956286967
UniRef90_A0A1X3K7C5|g__Escherichia.s__Escherichia_coli 1564615.7956286967
UniRef90_UPI000928192A 1214206.6654682336