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Old 10-29-2014, 02:49 AM   #1
Richa Sharma
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Question How to visualize microbiome datasets ?

Hi,

I have 16S rRNA datasets produced by Mothur and I want to plot my data and get publictaion quality figures (stacked bars, heatmaps, etc). I dont have familiarity with command line based packages such R, SAS, etc. I tried explicet, but it was not helpful for my data. Does anyone have suggestions for me about any user friendly tool, that I can use for my data?

Any help will be appreciated.

Richa
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Old 11-03-2014, 12:10 AM   #2
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Hi Richa,

have you tried STAMP (http://kiwi.cs.dal.ca/Software/STAMP)? You could also use some of the QIIME scripts (http://qiime.org/tutorials/tutorial.html).

cheers!
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Old 11-03-2014, 05:59 AM   #3
Richa Sharma
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Hi overflow,

Thanks for your suggestion. I dint hear about STAMP before. Are you sure if I can use it for mothur generated data? Because I did not see any explanation of mothur data file format in the STAMP guide book.
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Old 11-03-2014, 06:04 AM   #4
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there is a conversion tool for mothur data integrated (whatever that means because I'm not familiar with mothur).
However, at the end STAMP uses tables as input, so you should be able to import your data after some modifications.
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Old 11-04-2014, 04:06 AM   #5
Richa Sharma
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Hi overflow,

Thanks for help. I work with windows. I installed STAMP, and I was also able to make SPF file (from mothur files) using it, but when I try to load them, I cant see anything on STAMP window. Do you already use STAMP? Does it needs JAVA too ? What could be the problem ?
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Old 11-04-2014, 04:09 AM   #6
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just had the same problem, did you also include a metadata file?
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Old 11-04-2014, 05:05 AM   #7
Richa Sharma
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No I did not include a metadeta file.
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Old 11-04-2014, 05:08 AM   #8
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You could give that a try:
https://snowman.genome.tugraz.at/snowman/
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Old 11-04-2014, 05:19 AM   #9
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for PCA etc. you need to supply a metadata file, otherwise you will only be able to compare 2 samples
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Old 11-04-2014, 06:34 AM   #10
Richa Sharma
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I understand, for PCA, I must provide a metadta file. But I wanted to start with plotting simple bar graphs. where is the problem. Can you tell me ?
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Old 11-04-2014, 07:32 AM   #11
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ggplot2 heatmaps are IMO quite suitable for big data representation..
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Old 11-06-2014, 12:22 AM   #12
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Quote:
Originally Posted by Richa Sharma View Post
I understand, for PCA, I must provide a metadta file. But I wanted to start with plotting simple bar graphs. where is the problem. Can you tell me ?
supply metadata file and it will work, no idea why you have to do that...
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Old 12-15-2015, 08:36 AM   #13
julcham1
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Hi,
Which metadata file do you load in STAMP to make it work with mothur files ?
Thanks,
Julien
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Old 02-09-2016, 09:14 AM   #14
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You could also make a biom file in mothur then use qiime scripts for visualization. I would recommend you try Nephele <https://nephele.niaid.nih.gov> which has easy to use pipelines based on mothur or qiime and produces graphical outputs.
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16s illumina analysis, heatmap, microbiome, mothur meta-analysis, statistical analysis

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