Using Shotgun metagenomics CSV file as feature in QIIME2/Galaxy

Hi @jkharofa,

Welcome to the forum!
QIIME 2 does not have a functionality to accept .csv tables as input, though it certainly has been on the developer's radar for a while (github issue). You will want your feature table to be in .biom format to import into QIIME 2. Probably your easiest bet is to ask your sequencing facility because they almost certainly had a .biom to begin with and then converted to .csv for you. If that is not an option you should be able to convert this to a .biom using the biom package that is already present in your QIIME 2 environment. According to another post here, something like this should work

biom convert -i table.tsv -o converted_table.biom --to-hdf5

Note that this example had the table in a .tsv format so if it doesn't work with your .csv, just save your table as .tsv and try again.

Good luck!

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