CONET- biom file formatting and content

[Ahmed Abdelfattah]

Dear all, 

I'm trying to do microbial associations analysis with conet v 1.1.1beta on cytoscape 3.6.1. Following exactly the steps described in the app tutorial, I only get to load my data from certain biom files. I guess the problem is associated with the content of the biom file itself since it works fine with raw (not filtered, split, or rarified) tables. I was wondering if anyone has encountered a similar issue and knows the solution. Also in GUI, when I get the error message, I can't see the content of the message, it just says error (that is why I didn't attach any).

I will be happy to provide more information but I really wish this app could work.

Thank you and any insight will be appreciated 

Ahmed

[piet molenaar]

Hi Ahmed,

I am cc-ing one of the authors that just responded to a question relating to the CoNet app.

Regards,

Piet

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

[faustk...@gmail.com]

Dear Ahmed,

There are 2 types of biom files, HDF5 and JSON. CoNet only supports HDF5. You can convert one type into the other with the biom converter: http://biom-format.org

Hope this helps,

Karoline