How can I concatenate clinical data to metagenomic results?

Question

[agata88]

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

Answer 1

[olorze]

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.