Formating picrust output for LEfSe
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5.3 years ago
espop23 ▴ 60

I have the table generated from picrust:

"matrix_type": "sparse","matrix_element_type": "float","shape": [328, 152],"data": [[0,0,23.0],[0,2,12.0],[0,5,252.0],[0,7,387.0],[0,8,53.0],[0,9,2.0],[0,11,936.0],[0,12,319.0],[0,13,330.0],[0,14,2.0],[0,15,116.0],[0,16,729.0] ...

and need some help reformatting the file to run LEfSe.

I need to have "|" between the levels & need to change sample IDs of your samples, to the group they belong to. I tried importing into Excel, but it just comes up as one line. Could someone please tell me how to import into Excel with the values in the columns? Or how to change the float?

(Apologies, not that good with this syntax)

Thanks!

picrust excel lefse microbiome • 1.8k views
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