I’m a new humann2 user and I’m still trying to understand some of the humann2 output:
I created the files “p144C_pathabundance.tsv” and “p144C_genefamilies.tsv” (among other files) with the command
humann2 --threads 1 --input p144C.fastq --output humann2_out/
p144C_pathabundance.tsv (14.9 KB)
p144C_genefamilies.tsv (925.2 KB)
Then, I retrieved the reactions using the command:
humann2_regroup_table --input p144C_genefamilies.tsv --groups uniref50_rxn --output /outputFolder
And got the file “p144C_regroup_uniref50_rxn.tsv”.
p144C_regroup_uniref50_rxn.tsv (190.9 KB)
Some of the reactions in the regroup file are part of pathways listed in the file “p144C_pathabundance.tsv”. But the majority of the reactions belong to pathways not listed in the pathabundance file.
One example: The reaction GDPMANDEHYDRA-RXN is listed in file “p144C_regroup_uniref50_rxn.tsv”, but any of the pathways that have this reaction in it, are listed in the file “p144C_pathabundance.tsv”.
Here a few more reactions with this behavior:
‘APYRASE-RXN’, ‘ARGININE–TRNA-LIGASE-RXN’, ‘ARGINYLTRANSFERASE-RXN’, ‘ARGSUCCINSYN-RXN’, ‘ASNSYNA-RXN’, ‘ASNSYNB-RXN’, ‘ASPAMINOTRANS-RXN’, ‘ASPARAGINE–TRNA-LIGASE-RXN’, ‘ASPARTASE-RXN’, ‘ASPARTATE–TRNA-LIGASE-RXN’, ‘ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN’, ‘ASPARTATEKIN-RXN’, ‘ASPCARBTRANS-RXN’, ‘ATP-PYROPHOSPHATASE-RXN’, ‘ATPASE-RXN’, ‘ATPPHOSPHORIBOSYLTRANS-RXN’, ‘ATPSYN-RXN’, ‘BETA-LYSINE-56-AMINOMUTASE-RXN’, ‘BETAGALACTOSID-RXN’, ‘BIOTIN-CARBOXYL-RXN’, ‘BIOTINLIG-RXN’, ‘BRANCHED-CHAINAMINOTRANSFERILEU-RXN’, ‘BRANCHED-CHAINAMINOTRANSFERLEU-RXN’, ‘BRANCHED-CHAINAMINOTRANSFERVAL-RXN’, ‘BTUR2-RXN’
Could you please help me to understand the reason for this behavior?
Thank you.