Calculating pathway abundances from modified RXN/UniRef90 files

Microbial community profiling HUMAnN
1

Hello,

I would like to calculate pathway abundances using a TSV file of RXN abundances (or UniRef90 abundances), following the HUMAnN v3.8 process. Actually, my RXN abundance file is derived from the standard HUMAnN workflow, but I have manually removed the abundance contributions from a specific species. I want to use this method to confirm the impact of that species on pathway abundances.

I understand that stratified pathway abundance can, to some extent, answer my question, but I believe the results from these two approaches should be different. Unfortunately, I haven’t found a similar functionality in HUMAnN. Could you please help me with this? Is there a way to achieve this within HUMAnN, or would I need to modify the code?

Thank you very much for your assistance!

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The best way to do this would be to remove the unwanted species from the genefamilies.tsv files: remove the stratified rows and subtract their contributions from the totals as well. You can then give a genefamilies.tsv file as input to HUMAnN and it will quickly recompute the reaction and pathway abundances, but with the unwanted species excluded this time.

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