Biom files won't load correctly (or at all)

[Jessica Jarett]

I’m working with some biom files produced by itagger, and having problems getting them to load and display properly. The biom files directly outputted by itagger will load, but almost all of the samples and taxa are not shown, even though they seem to be detected as samples (see screenshot). Biom files that I have added metadata to using biom add-metadata don’t load at all. The loading progress bar will go to 100%, then nothing happens.

I looked at the example data provided, and noticed that my tables are in dense biom format, and have “int” rather than “float” for the matrix element type. Could this be causing the problem? Other than that nothing jumps out at me as being obviously wrong with my files.

Any suggestions would be appreciated, I can send the files in question if needed. Thanks!

[Holly Bik]

Hi Jess,

Sorry for the tardy reply - did you find a solution yet? 

Do you have access to the raw OTU map (e.g. the output of OTU picking in QIIME)? If so, could you try making an OTU table from scratch using the make_otu_table.py script (using the -t flag to add in the taxonomy from your taxonomy mapping file) - http://qiime.org/scripts/make_otu_table.html - after this you can go on and add the metadata to the resulting OTU table using the biom add-metadata command.

Let's see if that works - if not, can you send me the .biom file so I can have a look at it myself?

Thanks,

Holly

[Holly Bik]

Also - a second thing to try would be to convert your .biom file to "sparse" format. This might the problem, because "dense" files are pretty big (and I think the QIIME make_otu_table.py would give you a sparse .biom file by default) Conversion instructions are here: http://biom-format.org/documentation/biom_conversion.htm