Biom file will not load correctly

[pfa...@gmail.com]

Hello,

I am having trouble getting my biom file to load correctly. The screen that comes up after I select to load the file is completely blank except for a column of the left that shows my experimental treatments. When I select "proceed to gallery", I can see results on every page  except for attributes. However, some of my files have been named correctly while others are just given numbers. I will attach the biom file I am using so that you can see what is going on for yourself. 

Any help you could provide would be of assistance. 

[Holly Bik]

I tested the file and confirmed it wasn't working - not sure why the sample list isn't showing. I've had similar problems before and have been unable to pinpont the problem - I suggest converting your BIOM file back to a classic OTU table, and then re-converting back to BIOM (maybe some field got changed during the initial generation that is interfering with Phinch). Commands to run are as follows:

biom convert -i original_file.biom -o classic_OTUtable.txt -b --header-key=taxonomy

biom convert -i classic_OTUtable.txt -o new_BIOM_file.biom -m mapping_file.txt --table-type="otu table" --process-obs-metadata=taxonomy

biom add-metadata -i new_BIOM_file.biom -o new_BIOM_file_with_metadata.biom -m mapping_file.txt

Then try to load in Phinch again - Let me know if this works!

[Haley Pfaffe]

Thank you for getting back to me so quickly Holly! Your suggestion worked perfectly!! 

Thanks again,

Haley