I have a few projects using shotgun metagenomics sequencing. I receive data from our microbiome core in a CSV file. Is it possible to use this data within the QIIME2/galaxy environment to perform downstream analyses- diversity, relative abundance, etc? I am trying to understand how best to load this into galaxy as a feature table with a separate metadata file. My CSV files are in the following format:
Do I need to convert from CSV to another file type?
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.
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