Hi,
May I ask you a question about regrouping genes to other functional categories, for example to enzyme commission (EC).
The command I used is
humann2_rename_table --input path/to/genefamlies.tsv --custom /install/databases/humann2/Mapping/map_level4ec_name.txt.gz --output path/to/ec.tsv
My problem is:
For example, I have 6 samples and there is abundance of gene family (UniRef90_I3WJE2) for g__Bifidobacterium.s__Bifidobacterium_bifidum. However, after regrouping to EC, there is no any value for each sample (last row of attached table).
I checked the EC mapping file, there is UniRef90_I3WJE2 and UniRef90_I3WHB9 for EC 3.2.1.52.
May I ask why there is no value for any samples after regrouping?
Result from humann2
Sample1
Sample2
Sample3
Sample4
Sample5
Sample6
UniRef90_I3WJE2|g__Bifidobacterium.s__Bifidobacterium_bifidum
8.86E-06
1.72E-05
0
2.20E-07
1.79E-05
0
UniRef90_I3WHB9|g__Bifidobacterium.s__Bifidobacterium_bifidum
7.19E-06
1.43E-05
0
2.01E-07
1.17E-05
0
After regrouping to EC
3.2.1.52: Beta-N-acetylhexosaminidase|g__Bifidobacterium.s__Bifidobacterium_bifidum
0
0
0
0
0
0