question about loading on the web

[Jack L. D.]

Hey all,

so, I am having trouble uploading biom file from qiime onto the server.. the file might be too big?  is there anyone i can send this to and take a look at?

Thanks,
~JD

[Holly Bik]

Hi JD,

Do your .biom files have both taxonomy and sample metadata added in? Phinch won't be able to parse the files without this information - instructions on how to add this in are in the "Help" tab in the upper right hand corner of the website. The some .biom files that come out of QIIME have already taxonomy added in, but you need to manually add in your metadata from the QIIME mapping file using biom add-metadata command (in qiime 1.8) or add_metadata.py (in qiime 1.7 and below).

If this still doesn't get your file working, please let me know.

Holly

[Jay D.]

Hello Holly,

I have a bunch of biom files (through pick_open and core_diversity). I believe I have both (i know for sure about taxonomy, and is metadata just the sample id?).

I tried to use the instruction from "help" with the biom file from pick_open.  From "make_otu_table.py" i got "IndexError: list index out of range"  I guess that is an error to QIIME command...  

Nonetheless, do you want me to send you a copy of the biom file to make sure its in the correct format?

[Holly Bik]

Sorry for the slow reply, I've been traveling this week.

Metadata is NOT the sample ID - this info would contained in your QIIME mapping file (tab delimited text file prepared according to these instructions on the QIIME site: http://qiime.org/documentation/file_formats.html ), You would need to embed this in your .biom file using the biom add-metadata command, as follows:

biom add-metadata -i otu_table_mc2_w_tax.biom -o otu_table_mc2_w_tax_and_metadata.biom -m sample_metadata_mapping_file.txt

The output file from this command would then be ready to upload into Phinch. Let me know if you still have problems after embedding in your metadata.

[Jay D.]

Wow!  Thanks! That worked out great!

~JD

[Jay D.]

Though, I did experience pop up window saying something like "Phinch is not loading correctly"  also, when I tried to export image, it was not always able to download image... Also, I think the order of the charts was not the same as the description... All in all, this is one of the coolest graphing tool I've seen... I can finally display my data in a much clear way! 

~JD

[Holly Bik]

Yes, thanks for noticing that - we've got a bug on the live site right now where each of the visualizations is off by one (and clicking on the taxon bar chart will give you an error). The export image feature also seems to have a bug. 

We'll fix these things ASAP - thanks for your patience, we're still working out the last minute kinks!

Holly