Hi! I was wondering if it was possible to generate a table of ASVs and the sequences they represent. I'm able to get tables of ASVs and taxonomy but not one mapped to the unique samples. Could perhaps this be made using the BIOM format?
Thanks!!
Hello @jecohen,
Can you give me an example table you are looking for?
Like this?
| FeatureID | seq |
|---|---|
| asv1 | ACGATGATGCTGAC |
| asv2 | ACGATGATGCTCCC |
| asv3 | ACGATGATGGGTTT |
Or like this?
| FeatureID:SampleID | S1 | S2 | S3 | S4 |
|---|---|---|---|---|
| asv1 | 2 | 2 | 4 | 5 |
| asv2 | 2 | 2 | 40 | 5 |
| asv3 | 22 | 24 | 4 | 5 |
Colin,
My apologies for the late reply, I was not notified of your response! I was hoping to generate a table like the first one you posted- FeatureID and seq. Thanks!
Try this:
qiime feature-table tabulate-seqs \
--i-data ./dada2_rep_set.qza \
--o-visualization ./dada2_rep_set.qzv
Example output:
That example is from the Taxonomy section of the PD-mouse tutorial.
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Colin,
This worked! Thanks for your help with this issue!
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