mothur

Mothur: format to use Picrust

HI,
I want to produce the correct biom. file to have an OTUs table that ill use in Picrust. I saw this command (https://www.mothur.org/wiki/Make.biom) but something went wrong with Picrust and i cant continue. It would be useful a help, i’d really appreciate that.

Hi there,

Can you check out this thread and see if it helps?

Pat

Hi Pat, i’ve already seen this and tried, but it seems that there is something wrong with Picrust to do the “Predict Metagenome”. The output appears all upset and confused with the data. I think that i have the right OTU table, but maybe is in the wrong format for Picrust; im a bit confused.
Thank you for the answer, ill wait for yours tips and i hope ill be able to solve the problem.
Have a nice day.
Francesco

Sorry - that’s all I’ve got. I’m not a big fan of picrust and aside from one or two papers where we compared it to real metagenomic data we haven’t been using it. You might try picrust2, which might have an easier interface.

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Thank you so much however, ill try to use Picrust2. The imput files should be the same from mothur, isnt it ?

Hi-Hope this tutorial will help you to get correct biom output for the picrust.

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You might want to check to see if when you are making your biom file that the file converts into the expected format. I can’t access the wiki right now but there should be an option when writing up the command to select that the biom output should be in hdf5 or json format. If one didn’t work try the other?

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