How to convert the otu table in HMP QIIME project BIOM format compatible?

[Ali shojaee Bakhtiari]

The following link, I presume is the end result of applying QIIME on the hmp

ftp://public-ftp.hmpdacc.org/HMQCP/otu_table_psn_v35.txt.gz

When I read through the file using excel, I see the otu counts as expected, however when I try to read the file using the read_biom, I receive an error

 x <-read_biom("v35_psn_otu.genus.fixed.txt")

Error in fromJSON(content, handler, default.size, depth, allowComments,  : 

  invalid JSON input

I suppose the txt file should be converted to a biom file before the above line works, the question is how?

Thanks

[jonsan]

Hi Ali,

Is read_biom a function in R?

It sounds like the function is looking for a JSON-formatted biom file, and the provided otu table is a 'classic' delimited text OTU table.

If you have biom-format installed, you can easily perform this conversion according to the instructions provided here. 

Cheers,

-jon

[Ali shojaee Bakhtiari]

Thanks Jon. I found another link leading to the same solution. It must be correct.

Ali

https://github.com/joey711/phyloseq/issues/443

[jonsan]

Great, hope it works for you! Let us know if not.

Cheers,

-jon