# Kegg on Humann2 **URL:** \ **Category:** HUMAnN\ **Created:** [March 6, 2020, 5:18pm UTC](https://forum.biobakery.org/t/kegg-on-humann2/259 "2020-03-06T17:18:13Z")\ **Posts on this page:** 16\ **Page:** 1
**Author:** ![dbivona](https://avatars.discourse-cdn.com/v4/letter/d/ccd318/32.png) [@dbivona](https://forum.biobakery.org/u/dbivona)\ **Post date:** [March 6, 2020, 5:18pm UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/1 "2020-03-06T17:18:13Z")
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 ---
**Author:** ![npatin](https://avatars.discourse-cdn.com/v4/letter/n/c77e96/32.png) [@npatin](https://forum.biobakery.org/u/npatin)\ **Post date:** [March 23, 2020, 1:19pm UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/2 "2020-03-23T13:19:16Z")
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 Most of the online instructions for this process seem outdated.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 ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [April 1, 2020, 3:29pm UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/3 "2020-04-01T15:29:16Z")
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on how to generate KEGG pathway output using Legacy HUMAnN 1.0 functionality, but I agree that those results would be outdated at this point.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. ---
**Author:** ![erichx](https://avatars.discourse-cdn.com/v4/letter/e/c5a1d2/32.png) [@erichx](https://forum.biobakery.org/u/erichx)\ **Post date:** [May 7, 2020, 9:54pm UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/4 "2020-05-07T21:54:04Z")
> [@franzosa](#): > > `regroup` script to convert UniRef abundance to KO abundance 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\* ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [May 8, 2020, 2:05pm UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/5 "2020-05-08T14:05:18Z")
If you have a HUMAnN 2.0 install you can get these with the `humann2_databases` script (look for the “utility\_mapping” option). ---
**Author:** ![erichx](https://avatars.discourse-cdn.com/v4/letter/e/c5a1d2/32.png) [@erichx](https://forum.biobakery.org/u/erichx)\ **Post date:** [May 13, 2020, 3:22pm UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/6 "2020-05-13T15:22:15Z")
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! ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [May 14, 2020, 2:21pm UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/7 "2020-05-14T14:21:07Z")
@erichx Gotcha. Here is a link to all the mapping files: [http://huttenhower.sph.harvard.edu/humann2\_data/full\_mapping\_1\_1.tar.gz](http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_1_1.tar.gz) ---
**Author:** ![wfgui](https://avatars.discourse-cdn.com/v4/letter/w/67e7ee/32.png) [@wfgui](https://forum.biobakery.org/u/wfgui)\ **Post date:** [June 5, 2020, 1:21am UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/8 "2020-06-05T01:21:35Z")
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! ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [June 10, 2020, 3:56am UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/9 "2020-06-10T03:56:39Z")
Mappings from UniRef to other systems (including KEGG) are sourced from UniProt’s annotations of the representative proteins. ---
**Author:** ![Kena\_Sharma](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/kena_sharma/32/358_2.png) [@Kena\_Sharma](https://forum.biobakery.org/u/Kena_Sharma)\ **Post date:** [August 25, 2020, 5:08am UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/10 "2020-08-25T05:08:36Z")
Hi, I want to get the abundance value for KEGG pathway as well. At the moment, I am able to get the KO ids from uniref90. In order to get the KEGG pathway abundance, what should be my next step? When you say download and “reformat” the pathway, what does that mean exactly? > [@franzosa](#): > > download and reformat modern KEGG pathways ---
**Author:** ![alienzj](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/alienzj/32/70_2.png) [@alienzj](https://forum.biobakery.org/u/alienzj)\ **Post date:** [September 21, 2020, 2:10am UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/11 "2020-09-21T02:10:58Z")
Hi, does HUMAnN 3.0 support this feature ? ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [September 22, 2020, 2:17pm UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/12 "2020-09-22T14:17:56Z")
HUMAnN 3.alpha is currently packaged with HUMAnN 2-era MetaCyc pathways. I’m hoping to add newer MetaCyc pathways and KEGG modules to the non-alpha release. ---
**Author:** ![wfgui](https://avatars.discourse-cdn.com/v4/letter/w/67e7ee/32.png) [@wfgui](https://forum.biobakery.org/u/wfgui)\ **Post date:** [January 20, 2021, 7:55am UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/13 "2021-01-20T07:55:33Z")
I can see a lot of mapping files in full\_mapping directory,but the mapping file of MetaCyc Reactions could not be found.Can you provide a link to download it? Thanks! Mapping files in full\_mapping directory: ```auto map_ec_name.txt.gz map_go_name.txt.gz map_ko_uniref50.txt.gz map_pfam_name.txt.gz map_uniref50_uniref90.txt.gz map_eggnog_name.txt.gz map_go_uniref50.txt.gz map_ko_uniref90.txt.gz map_pfam_uniref50.txt.gz map_uniref90_name.txt.bz2 map_eggnog_uniref50.txt.gz map_go_uniref90.txt.gz map_level4ec_uniref50.txt.gz map_pfam_uniref90.txt.gz uniref50-tol-lca.dat.bz2 map_eggnog_uniref90.txt.gz map_ko_name.txt.gz map_level4ec_uniref90.txt.gz map_uniref50_name.txt.bz2 uniref90-tol-lca.dat.bz2 ``` ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [January 25, 2021, 12:31am UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/14 "2021-01-25T00:31:26Z")
The MetaCyc reaction mapping is packaged under the pathways/ folder since mapping from UniRefs to reactions is part of pathway quantification. The regroup\_table script knows to look for that specific file in the pathways/ location (to avoid storing it twice). ---
**Author:** ![jagut](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jagut/32/219_2.png) [@jagut](https://forum.biobakery.org/u/jagut)\ **Post date:** [April 2, 2021, 9:46am UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/15 "2021-04-02T09:46:19Z")
Hi guys, I’m using this thread as my question is linked to the utilization of the different types of mapping files packed with HUMAnN. I have annotated a bunch of predicted ORFs using eggNOG-mapper, and now I want to map the eggNOG ID to a single UniRef90/50 ID, but given that one eggNOG ID can be mapped to multiple UniRef IDs, the Q is then: how may I get a simple 1:1 mapping? Could you please give me some hints as to how to go about this, or perhaps point me to a dedicated script to achieve this? Thanks a lot for your feedback! ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [April 19, 2021, 4:22pm UTC](https://forum.biobakery.org/t/kegg-on-humann2/259/16 "2021-04-19T16:22:33Z")
As you say, because the UniRef:eggNOG mapping is many:1, there is no single best UniRef corresponding to a given eggNOG. You could alternatively annotate your ORFs directly against UniRef (e.g. by DIAMOND blastp’ing them against the HUMAnN database and taking ~the best hit for each one). That would give you something like a 1:1 mapping/pairing in that each ORF would then be mapped to 1 UniRef and 1 eggNOG.