hi!?
I am writing this because I have a question while using the humanN3 tool.
#One.
The function table was obtained using the human3 tool.
I want to compare metacyc pathways between Control and Case using LinDA.
Can I use total count without |g__Bacteroides.s__Bacteroides_caccae in this way?
Pathway 04003186_Abundance 04008856_Abundance
1CMET2-PWY 5976.246297 4933.886741
3-HYDROXYPHENYLACETATE-DEGRADATION-PWY 0 414.6064445
7ALPHADEHYDROX-PWY 0 0
AEROBACTINSYN-PWY 0 0
ALL-CHORIMATE-PWY 0 60.43152681
#2.
What should I do if the path is obtained but the microorganism I want to see does not exist, or if I want to know what function the microorganism I want to see (ex s__Bacteroides_vulgatus) has?
path $SAMPLENAME_Abundance
unmapped 140.0
87.0 unintegrated
Not integrated|g__Bacteroides.s__Bacteroides_caccae 23.0
Not integrated|g__Bacteroides.s__Bacteroides_finegoldii 20.0
Not Integrated|Unclassified 12.0
PWY0-1301: Melibiose decomposition 57.5
PWY0-1301: Melibiose decomposition|g__Bacteroides.s__Bacteroides_caccae 32.5
PWY0-1301: Melibiose decomposition|g__Bacteroides.s__Bacteroides_finegoldii 4.5
PWY0-1301: Melibiose Decomposition|Unclassified 3.0
PWY-5484: glycolysis II (from fructose-6P) 54.7
PWY-5484: Glycolysis II (derived from fructose-6P)|g__Bacteroides.s__Bacteroides_caccae 16.7
PWY-5484: Glycolysis II (from fructose-6P)|g__Bacteroides.s__Bacteroides_finegoldii 8.0
PWY-5484: Glycolysis II (from fructose-6P)|Unclassified 6.0