The bioBakery help forum

Kegg on Humann2

Hi,

I was wondering if there was a way to get the keggpathways from Humann2 without installing Humann legacy. I am trying to confirm data I obtained containing metacyc pathways.

Is this possible without using the humann_legacy program and if that isnt the case, does anyone know where I can find a KEGG database folder to implement?

Best,
Dan

I am also interested in mapping the MetaCyc output to KEGG pathways. Most of the online instructions for this process seem outdated. Any help would be appreciated!

Thanks,
Nastassia

HUMAnN 2.0 does not automatically generate KEGG pathway output. The manual provides instructions on how to generate KEGG pathway output using Legacy HUMAnN 1.0 functionality, but I agree that those results would be outdated at this point.

If you are able to download and reformat modern KEGG pathways on your own, you can use the regroup script to convert UniRef abundance to KO abundance and then provide KO abundance + KEGG pathway definitions to HUMAnN 2.0 to compute pathway abundance.

We’re looking into including KEGG pathways + modules as a MetaCyc alternative in the next iteration of HUMAnN.

Hi Eric,
Can you provide a link to download the following mapping files to use the regroup script? Thank you.

Mappings are available for both UniRef90 and UniRef50 gene families to the following systems:

** MetaCyc Reactions*
** KEGG Orthogroups (KOs)*
** Pfam domains*
** Level-4 enzyme commission (EC) categories*
** EggNOG (including COGs)*
** Gene Ontology (GO)*
** Informative GO*

If you have a HUMAnN 2.0 install you can get these with the humann2_databases script (look for the “utility_mapping” option).

I’m using Galaxy platform. The regroup script need to supply the mapping file manually. I’m wondering is there anyway to download the database. I found a similar thread in old Google Groups discussion, but the link you provided there has expired. Thank you!

@erichx Gotcha. Here is a link to all the mapping files:

http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_1_1.tar.gz

Thanks for humann2, I have a question here:you provide a uniprotID <-> KO or GO mapping for uniref90 and uniref50. How did you obtain those?

Thanks!

Mappings from UniRef to other systems (including KEGG) are sourced from UniProt’s annotations of the representative proteins.