The bioBakery help forum

Example for `File Type 4 (gene table) tsv` as input to HUMAnN?

I am unable to find an example file for how the input for a gene table should look like as an input for HUMAnN.
Is there an example file somewhere?
Can I use output from mapped from GMGC ?

Thanks!
Harithaa

Hi,

The command is

humann -i genetable.tsv  --input-format genetable -o functions --diamond ../../

A gene table looks like this,

# Gene Family   E100002696_L01_1_kneaddata_Abundance-RPKs
UNMAPPED        4887640.0000000000
UniRef50_A0A125UBK5     2135.6903965600
UniRef50_A0A125UBK5|g__Escherichia.s__Escherichia_coli  1652.1739130435
UniRef50_A0A125UBK5|g__Enterococcus.s__Enterococcus_faecalis    483.5164835165
UniRef50_A0A1D7PV13     2135.6122163071
UniRef50_A0A1D7PV13|g__Escherichia.s__Escherichia_coli  2135.6122163071
UniRef50_F4NR79 1762.3762376238
UniRef50_F4NR79|g__Escherichia.s__Escherichia_coli      1762.3762376238
UniRef50_Q54HB2 1585.8948562197
UniRef50_Q54HB2|g__Neisseria.s__Neisseria_sp_oral_taxon_014     464.2864737279
UniRef50_Q54HB2|g__Aggregatibacter.s__Aggregatibacter_segnis    436.5079365079
UniRef50_Q54HB2|g__Neisseria.s__Neisseria_macacae       354.8387096774
UniRef50_Q54HB2|g__Neisseria.s__Neisseria_subflava      124.4813278008
UniRef50_Q54HB2|g__Escherichia.s__Escherichia_coli      105.9552692206
UniRef50_Q54HB2|g__Neisseria.s__Neisseria_canis 66.6666666667
UniRef50_Q54HB2|g__Eikenella.s__Eikenella_corrodens     23.5191637631