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LangilleLab / microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
GNU General Public License v3.0
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Normalizing data obtained from other software? #44

Closed Jigyasa3 closed 4 years ago

Jigyasa3 commented 4 years ago

Hey!

Is it possible to incorporate a relative abundance file into humann2 for downstream analysis? For example, I have an insect gut metagenome data which I have annotated via COG and Pfam database. I also have the taxonomic information via MEGAN package. Furthermore, I have converted the raw counts into reads per million for each function and taxa.

But I want to incorporate the gap-filling step in humann2 and compression constant to account for gene copy number and pathway copy number non-linearity. (https://bitbucket.org/biobakery/humann2/wiki/Home#markdown-header-2-pathway-abundance-file).

I was wondering if there is a "cheat" way of doing these normalizations without re-running the analysis from scratch?

Thanks!

gavinmdouglas commented 4 years ago

Hi there,

You can definitely input gene family tables to HUMAnN2 so that you can just run the pathway inference step (and select gap filling) without needing to re-run the entire pipeline from scratch. You might have more luck on the HUMAnN2 forum with specific questions in the future though by the way.

Best,

Gavin

Jigyasa3 commented 4 years ago

Thank you @gavinmdouglas !