SparCC Tutorial/User Manual?

[brett...@gmail.com]

Hello QIIME Team,

I tried to google this and also read through the references to SparCC within this forum, but could not find any good information on how to use SparCC for co-occurance analysis of my OTUs.

I fully realize that SparCC is not a part of QIIME, but you have been very helpful with information regarding sequencing analysis, so I was hoping that you might have some clues.

Long story short, can you refer me to any resources that would help me get started utilizing SparCC? Ideally a walkthrough would be best, but even a list of file types needed and steps involved would be a start.

Thanks a ton!

Brett

[Jamie Morton]

Hi Brett,

I found the README bundled with the source code a good place to start.  It also includes some example files that you can test out.

Let me know if you need any more information.

Best,

Jamie

[Brett Loman]

Thanks Jamie,

This probably sounds pretty lame, but I found the site and looked through the readme that you are referencing here and I have a general idea of what to do, but I don’t even know how to install SparCC from that page to begin with. I also found one other resource that very vaguely walks through an analysis example found here http://psbweb05.psb.ugent.be/conet/microbialnetworks/sparcc.php

This all leaves me with a few questions:

1. How do I install SparCC?
2. Is the  initial input .txt file an OTU table as can be generated via the info found here? http://biom-format.org/documentation/biom_conversion.html 
3. Once the p-values are calculated as in the example, do you know of a good way to visualize them? I am familiar with Cytoscape, if that is possible. I have over 1000 OTUs, so I feel like simply sorting through the resulting .txt files would be pretty time consuming…

I realize that this may seem rather basic and/or out of your domain, but that is why I was wondering if anyone knew of other resources. In any case, I appreciate the help!

Best,

Brett

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[Will Van Treuren]

Hi Brett, 

A colleague and I have been evaluating SparCC vs other co-occurrence detection tools for use with microbiome data. I may be able to help with your questions:

> 1. How do I install SparCC?

SparCC is installed like many python program son *nix systems; you have to let the computer know the path to the executables as well as the path to the library files which undergird the executables. The executables need to be visible via your PATH variable. So, for instance, in my .bash_profile I have the following line:

PATH=$PATH:/Users/wdwvt/src/sparcc/

export PATH

The shell also needs to know where the library files live, which the following line in .bash_profile takes care of:

PYTHONPATH=$PYTHONPATH:/Users/wdwvt/src/sparcc/

export PYTHONPATH

If you are unsure of how the PATH and PYTHONPATH variables work, its important to learn those, otherwise your installation of SparCC and other *nix tools will fail. Note that the '/Users/wdwvt/src/' portion of my paths above is unique to my system - you'll have to specify where you put sparcc in your system. 

> Is the  initial input .txt file an OTU table as can be generated via the info found here?

Yes, make sure that its a 'classic' OTU table format. There can be only one column and one row of text (the otus names, and the sample names, respectively). A final column of text with 'taxonomy' in it (as a common example) will cause errors.  Similarly, sometimes a classic OTU table will look like:

#weird comments or converted by message

#OTU    sample1    sample2 ...

...

The first comment line must be removed. 

> Once the p-values are calculated as in the example, do you know of a good way to visualize them? I am familiar with Cytoscape, if that is possible. I have over 1000 OTUs, so I feel like simply sorting through the resulting .txt files would be pretty time consuming…

You can use the library we have been using for this. It gets you some sorting and visualization functions. It will need to be installed in the same way as the SparCC stuff (though there are no scripts that require modification of the 'PATH' variable). If you are not keen on diving into the code, Cytoscape is your best answer. You can use this tutorial to get you started. 

Hope this helps,

Will 

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[Colin Brislawn]

Hello Brett,

As far as I can tell, SparCC is just a bunch of python scripts, so you don't have to install anything. You can just clone and run the scripts.

hg clone https://bitbucket.org/yonatanf/sparcc

cd sparcc

python SparCC.py example/fake_data.txt -i 5 --cor_file=example/basis_corr/cor_sparcc.out

Colin

[Brett Loman]

Will and Colin,

Thank you both so much for the very fast replies!

I will utilize the information below and see how it goes; it seems very helpful!

Best,

Brett