Hmp_pathabund.pcl

Microbial community profiling HUMAnN
1

Hello,

I would like to know how to get to the * [hmp_pathabund.pcl] format mentioned in: (https://raw.githubusercontent.com/biobakery/biobakery/master/test_suite/biobakery_tests/data/humann/input/hmp_pathabund.pcl).
The tutorial moves from .tsv files with no metadata included to this other format. Seems like there is a missing step perhaps?

Thank you very much!
Kind regards,
M

2

Sorry for the slow reply. Making this table isn’t a part of the HUMAnN workflow per se. You would need to first merge your per-sample profiles into a multi-profile table (we do bundle utility scripts with bioBakery for doing this step). You would then need to merge your metadata table onto the multi-profile table, typically using the sample ID as a key for merging.