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How can I concatenate clinical data to metagenomic results?

Hi all,

I would like to find a correlation between my metagenomic results from Qiime (otu_table.biom) and some clinical data.

Any suggestion how to do that?

Is there a tool that can make some plots? Or should I run some stats by myself?

I was trying to run:

make_otu_heatmap.py -i otu_table.biom -o heatmap_grouped_by_Treatment.pdf -m mapping_file.txt -c Treatment

but it seems there is a bug and it's impossible to do that.

Thanks in advance,

Agata

metagenomic
• 1,671 views • link
updated by olorze • olorze • written by agata88 agata88

1 answer

Before you call something a bug... um okay, shortly speaking, you need to give more information. I assume your input file "otu_table.biom" is valid and the qiime package is installed correctly and other scripts work fine.

  • What exactly happens when you run that command?
  • Have you validated the "mapping_file.txt"?
  • Have you confirmed that the "otu_table.biom" file is integrated with metadata ($ biom add-metadata ...) and contains the "Treatment" column? You can view your biom file with a hdf5 file reader, e.g. hdfview, or obviously, in python or R or something.
  • The tool for what I think you might looking for is differential_abundance.py. Take a look?

I run the command you used on some data on my computer and if works just fine. Not sure if you're still looking for help though...

Cheers.

• 0 views • link
written by olorze • olorze

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