Obtain the pathway abundance file for some specific EC

Microbial community profiling HUMAnN
1

Hi, I have a list of ECs that I’m interested in and I want to get the related pathway abundance file.
I’ve noticed that HUMAnN will produce the pathway abundance file as the default output. However, this is the result of all genes.

  1. So I’m wondering, is it possible that I produce a pathway abundance file only related to the EC list I have?

  2. Or is there a way that I provided a list of genes that are related to these ECs as the input then I have the corresponding pathways abundance file?
    I know there is a mapping file of reaction-pathway mapping file: metacyc_structured_pathways_filtered provided. However in this file, it has ( or , in the reaction, I don’t know how to integrate it.

Thank you.

2

Sorry for the slow reply. You can provide a genefamilies.tsv file to HUMAnN as input and it will use it to create pathways (picking up in the middle of the normal workflow). If you pass a curated lists of UniRefs as such a file - corresponding only to your ECs of interest - then HUMAnN would only use those UniRefs/ECs to reconstruct pathways.

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