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-   -   How to visualize microbiome datasets ? (http://seqanswers.com/forums/showthread.php?t=47862)

Richa Sharma 10-29-2014 02:49 AM

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

overflow 11-03-2014 12:10 AM

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!

Richa Sharma 11-03-2014 05:59 AM

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.

overflow 11-03-2014 06:04 AM

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.

Richa Sharma 11-04-2014 04:06 AM

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 ?

overflow 11-04-2014 04:09 AM

just had the same problem, did you also include a metadata file?

Richa Sharma 11-04-2014 05:05 AM

No I did not include a metadeta file.

ulz_peter 11-04-2014 05:08 AM

You could give that a try:
https://snowman.genome.tugraz.at/snowman/

overflow 11-04-2014 05:19 AM

for PCA etc. you need to supply a metadata file, otherwise you will only be able to compare 2 samples

Richa Sharma 11-04-2014 06:34 AM

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 ?

rhinoceros 11-04-2014 07:32 AM

ggplot2 heatmaps are IMO quite suitable for big data representation..

overflow 11-06-2014 12:22 AM

Quote:

Originally Posted by Richa Sharma (Post 153846)
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...

julcham1 12-15-2015 08:36 AM

Hi,
Which metadata file do you load in STAMP to make it work with mothur files ?
Thanks,
Julien

MQ-BCBB 02-09-2016 09:14 AM

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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