Combine HUMAnN gene families file for MaAsLin

Microbial community profiling HUMAnN
1

Hello!
I’ve been using HUMAnN 3.0 and I would like to use MaAsLin2 on the output file from HUManN.
I have completed the HUMAnN regroup, rename, renorm command and have the output as I need it.

Is there a way to combine the outputs? I have 8 samples, and therefore 8 HUMAnN outputs.

I saw this tutorial where they were combined in the “pathways_norm.tsv” file. https://github.com/karkman/MetagenomeCourse2019/blob/master/R_for_Humann2/pathways_norm.tsv

Is this something I would need to write my own script for?
Thank you for your time!
Emily

2

There is a humann_join_tables script that I think solves the problem you’re posing here?

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Thank you! I will try this!

For anyone else: I was able to merge everything in R.

I tried to delete my post after I figure it out, but I wasn’t able to!

4

No need to delete unless you really want to - this can still be useful to readers! :slight_smile:

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