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PitchInteractiveInc / Phinch

Phinch is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project represents an interdisciplinary collaboration between Pitch Interactive, a data visualization studio in Oakland, CA, and biological researchers at UC Riverside.
http://phinch.org/
BSD 2-Clause "Simplified" License
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De novo biom files #47

Open akknight opened 9 years ago

akknight commented 9 years ago

Hi, I am trying to visualize de novo picked OTUs with phinch and cannot seem to get the file to upload. It acts as though the upload is successful, but then nothing happens. I did include the metadata in the biom file. Does phinch support de novo picked OTUs? Thanks! Anna

hollybik commented 9 years ago

Hi Anna - yes, Phinch does support any type of OTU picking protocol. Usually failure to load indicates a formatting problem with the BIOM file (note that there are different versions of BIOM and Phinch currently only supports v1.0). Can you troubleshoot according to this thread and let me know what works? https://github.com/PitchInteractiveInc/Phinch/issues/46

akknight commented 9 years ago

Hi Holly,

Thanks for getting back to me. I am using QIIME version 1.8. I tried converting back to the classic file type per your suggestion on the google page, but it still will not load. I'm new to qiime, but as far as I can tell my biom table and map file look normal, and should have properly merged using the biom add-metadata command. I was able to successfully upload the closed reference OTUs, so I'm not sure where I'm going wrong.

hollybik commented 9 years ago

Just checking in to see if you got your file to work yet? If you've followed all the advice in the above Github thread and it's still not working, then the only way I can help further is if you send me the BIOM file that is giving you problems. Just make sure that the file is in BIOM 1.0 format (which is not the default output format if you are using QIIME 1.9)

akknight commented 9 years ago

Hi Holly, Thanks for checking in, I didn't get it to work, but I'm not using that file anymore. Thanks for your help!

gtan9 commented 7 years ago

Hi,

I followed the thread #46 but I have had problem adding metadata after converting to JSON format. I was able to add metadata with the original biom file before conversion using the same command. Do you have any suggestions how to troubleshoot this?