How to add taxonomy to feature-table.qza and get otu id of each taxonomy and number of otus

@Yanfei-Geng, I don’t think the data from alpha-rarefaction is exactly what you’re looking for. Does the following get you what you need? The table.qza file that I’m starting with is available here.

$ qiime tools export table.qza --output-dir ./
$ biom convert -i feature-table.biom -o feature-table.tsv --to-tsv
$ biom head -i feature-table.tsv
# Constructed from biom file
#OTU ID	L1S105	L1S140	L1S208	L1S257	L1S281
4b5eeb300368260019c1fbc7a3c718fc	2222.0	0.0	0.0	0.0	0.0
fe30ff0f71a38a39cf1717ec2be3a2fc	5.0	0.0	0.0	0.0	0.0
d29fe3c70564fc0f69f2c03e0d1e5561	0.0	0.0	0.0	0.0	0.0
868528ca947bc57b69ffdf83e6b73bae	0.0	2276.0	2156.0	1205.0	1772.0
154709e160e8cada6bfb21115acc80f5	812.0	1176.0	713.0	407.0	242.0 

Here, the first column contains feature or OTU ids (e.g., 4b5eeb300368260019c1fbc7a3c718fc), the first row contains sample ids (e.g., L1S105), and the values in the table indicate the number of times each feature was observed in each sample. So, in this case, feature 4b5eeb300368260019c1fbc7a3c718fc was observed 2222 times in sample L1S105, and zero times in each of the other samples.

1 Like

2 off-topic replies have been split into a new topic: What does the number represent in observed_otus.csv

Please keep replies on-topic in the future.

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.