Filtering contaminants


Please help I am trying to filter out contaminants in my table , I created a directory
qiime tools export --output-dir taxonomy-export taxonomy.qza
then I ran this script
grep -v -i “mitochondia|chloroplast|Feature” taxonomy.tsv | cut -f 1 > no-chloro-mito-ids.txt
I then exported my data to biom format using
qiime tools export --output-dir dada2-table-export table.qza
then ran the following script
biom subset-table
–input-hdf5-fp feature-table.biom
–axis observation
–ids no-chloro-mito-ids.txt
–output-fp feature-table-subset.biom
however i get an error message:ValueError: The following ids could not be found in the biom table: {‘Feature ID’}

Thanks in advance for your assistance

Hi @kedi! Have you had a chance to try out qiime taxa filter-table in QIIME 2? Check out this section of the filtering tutorial for examples. We can’t really provide much support for filtering taxa outside of QIIME 2 (e.g. with biom commands or shell commands).

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That was helpful, thanks!


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