13. Export Files - DianaCarolinaVergara/16S-rRNA-Analysis GitHub Wiki
Export final files
Explort with Qiime1
module load anaconda/python2
module load qiime/1.9.1
First you have to export the files .qza to the format .biom with the command qiime tools export
You select as input whatever .qza file you want with the command --input-path and the output path.
Then you have to convert the previous .biom file to a file capable to be read in Excel
.tsv , .txt
Some examples with our previous used files:
qiime tools export --input-path table-dada2.qza --output-path mantel
biom convert -i mantel/feature-table.biom -o mantel/otu_table.txt --to-tsv
qiime tools export --input-path collapsed_family_table.qza --output-path core-metrics-results
biom convert -i core-metrics-results/feature-table.biom -o core-metrics-results/otu_family_table.txt --to-tsv
qiime tools export --input-path collapsed_phylum_table.qza --output-path core-metrics-results
biom convert -i core-metrics-results/feature-table.biom -o core-metrics-results/otu_phylum_table.txt --to-tsv
qiime tools export --input-path taxonomy.qza --output-path core-metrics-results
biom convert -i core-metrics-results/feature-table.biom -o core-metrics-results/taxonomy.txt --to-tsv
Finally, another webpage to learn how to export different type of files:
And some info about the .biom format files.
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