Heatmap with relative abundances

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beatrizgi...@gmail.com

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Jul 15, 2016, 12:01:06 PM7/15/16
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Hi, 

I'm trying to do a heatmap with relative abundances instead of using the real OTU counts. Any clue how to do it? 

Thanks, 
Bea. 

Justine Debelius

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Jul 15, 2016, 1:04:28 PM7/15/16
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Hi Bea,

There's a QIIME script, normalize_tables.py which you can use to convert your OTU counts to relative abundance. 

You should then be able to make an heatmap using your normalized biom table.

Cheers,
Justine 

beatrizgi...@gmail.com

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Jul 18, 2016, 8:33:41 AM7/18/16
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Hi Justine, 

Thanks for the tip. I had a look of the script but I don't really know to convert the OTU counts to relative abundances. I mean, I don't know which argument I might use for it. 

-i, --input_path
Path to the input BIOM file (e.g., the output from OTU picking) or directory containing input BIOM files for batch processing [REQUIRED if not passing -l]
-o, --out_path
Output filename for single file operation, or output directory for batch processing [REQUIRED if not passing -l]
-s, --output_CSS_statistics
Output CSS statistics file. This will be a directory for batch processing, and a filename for single file operation [default: False]
-z, --DESeq_negatives_to_zero
Replace negative numbers produced by the DESeq normalization technique with zeros [default: False]
-a, --algorithm
Normalization algorithm to apply to input BIOM table(s). [default: CSS] Available options are: CSS, DESeq2
-l, --list_algorithms
Show available normalization algorithms and exit [default: False]



Thanks, 
Bea. 
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