I am trying to export a .biom file to eventually convert to . tsv file to use
LEfSe on ( https://huttenhower.sph.harvard.edu/galaxy/). I am able to do this just fine, but I am unable to get a file with the one line of metadata I am interested in actually feeding this program to be included (in my case, the sex of the person that each sample came from).
How does one export a .biom file with metadata included from qiime2? I’ve tried to add the meta data to the .biom file with a .tsv file, but it never actually adds (referencing
Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)). Can anyone provide any help?
You can try to add the meta-data on your own, as long as you match it with the correct sample:
I am currently looking for ways to analyse my 16s data using Maaslin and Lefse after performed QIIME2 analysis, does anyone did that before? I have problem in the beginning now in the installing and what is the input files from QIIME2 that I should use.
Thanks for the reply. Do you mean open the file and actually add the data? I could but it’s a lot a lot of samples. Do you know of a simpler way?
@ben and @msport469,
Im going to bump this over to the "other tools" category, since it deals with biom-specifically and not a QIIME2 plug in, but also maybe look at this, it at least specifies export with metadata.
I have convert the feature table which form with qiime2.2019.7 from .biom to .txt by biom, like this:[feature%20table]
Now I want to use STAMP to analyze my data. But the data that STAMP needs must be like this [stamp-otu] that include taxonomy class and the form must be strictly hierarchy.
Please tell me how to get the right form data that STAMP could use.
Thanks very much!!!
Or, if you're so inclined, the python API isn't bad for this.