Humann2_rename_table

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

This is a known issue that is flagged to be fixed in an upcoming HUMAnN2 release. The regroup_table script has a --precision flag that defaults to 0.001. Since you’re working with really small numbers (<0.001) you should set this flag to 0 so that the regrouped abundances don’t get rounded to 0. Sorry for the trouble!

Hi Franzosa, thank you very much to reply. It is good to know the reason and will try it.