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ToniWestbrook / paladin-plugins

Pipeline plugins for PALADIN, providing HPC support, abundance (taxonomy, go terms), customized reports, etc
MIT License
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metabolic pathway participation #1

Open gundizalv opened 5 years ago

gundizalv commented 5 years ago

Hi

How do you compute metabolic pathway participation? What's the manner? Can I convert the outputted values in a kind of measure comparable across the pathways and samples?

For example, pathway abundance measured in RPK o CPM (RPKM), as humann2 does: https://bitbucket.org/biobakery/humann2/wiki/Home#markdown-header-2-pathway-abundance-file

ivelsko commented 4 years ago

Hi,

I would also like to ask this. I'm trying to use PALADIN as an alternative to HUMAnN2 for samples that aren't human-associated, which are very poorly characterized by HUMAnN2.

I tried different settings on 1 sample and calculated totals row-wise and column-wise on the output, but the totals never sum up to 1 or 100, so I don't understand what the values in each cell represent. I tried :

paladin-plugins.py @@pathways -i sample1.upsp_uniprot.tsv -q 30 -l 6 @@write pathways_test_l6_output.txt
paladin-plugins.py @@pathways -i sample1.upsp_uniprot.tsv -q 30 -a 4 -l 6 @@write pathways_test_a4l6_output.txt
paladin-plugins.py @@pathways -i sample1.upsp_uniprot.tsv -q 30 -a 4 -l 3 @@write pathways_test_a4l3_output.txt
paladin-plugins.py @@pathways -i sample1.upsp_uniprot.tsv -q 0 -l 0 @@write pathways_test_q0l0_output.txt

The last one with -q 0 -l 0 I wanted to use all the data expecting that the column would sum to 100, indicating that the values are the % of total identified enzymes that fall in that pathway, but the total was 35.8.

Would you be able to provide an explanation of what's being calculated in this plug-in?