at the beginning, I only download the 2 database, at the end I found large percentage of unmapped pathway,
then I use
$humann_databases --download utility_mapping full DB
and rerun the program, there are still large percentage of unmapped pathway
Thanks for your kind attention
I’m not sure what you mean by “unmapped pathway”?
Thanks for your attention, Franzosa!
Below is a snippet from demo_pathabundance.tsv. As you can see, there’s a large proportion of unmapped and unintegrated pathways. We’ve observed the same issue in our real sample.
=====
| # Pathway | demo_Abundance |
|---|---|
| UNMAPPED | 11284.7425816747 |
| UNINTEGRATED | 28797.1613434528 |
| UNINTEGRATED | g__Bacteroides.s__Bacteroides_ovatus |
| UNINTEGRATED | unclassified |
| UNINTEGRATED | g__Alistipes.s__Alistipes_finegoldii |
| DTDPRHAMSYN-PWY: dTDP-β-L-rhamnose biosynthesis | 127.5869002337 |
| DTDPRHAMSYN-PWY: dTDP-β-L-rhamnose biosynthesis | g__Bacteroides.s__Bacteroides_ovatus |
| DTDPRHAMSYN-PWY: dTDP-β-L-rhamnose biosynthesis | g__Alistipes.s__Alistipes_finegoldii |
| PWY-1042: glycolysis IV | 107.2639971877 |
| PWY-1042: glycolysis IV | g__Bacteroides.s__Bacteroides_ovatus |
| PWY-1042: glycolysis IV | unclassified |
| PWY-5130: 2-oxobutanoate degradation I | 86.8968585593 |
| PWY-5130: 2-oxobutanoate degradation I | g__Bacteroides.s__Bacteroides_ovatus |
| PWY-6609: adenine and adenosine salvage III | 81.1265698140 |
| PWY-6609: adenine and adenosine salvage III | g__Bacteroides.s__Bacteroides_ovatus |
| PWY-5484: glycolysis II (from fructose 6-phosphate) | 69.6332561451 |
in our microbiome samples
Mapped Pathways: ~15%
UNINTEGRATED: ~40%
UNMAPPED: ~32%
hope this is normal output? not indicate sample or method mistake?
cheers