Hi,
Anyone one knows if there is a way of knowing how much reads my principal taxa are responsible for?
Thank you
Hi,
Anyone one knows if there is a way of knowing how much reads my principal taxa are responsible for?
Thank you
Hi @annsantos,
I would use the qiime feature-table filter-feature
using your taxonomy file as metadata or a modified taxonomy file as metadata that lists your principle taxa.
Best,
Justine
Thank you for your reply!
Than i have to transform in qzv for visualization or export to a tsv file?
Iam asking this because i had errors with the two options.
Hi @annsantos,
If have you run qiime metadata tabulate
, then you can download as a tsv.
We can help you debug, but you need to post the error messages.
Best,
Justine
Hi @jwdebelius,
My code was:
qiime feature-table filter-features
--i-table table.qza \ table from dada2
--m-metadata-file table-no-mitochondria.qza \ #my taxa
--o-filtered-table sample-contingency-filtered-table.qza
Than, i did this:
qiime metadata tabulate \
--m-input-file sample-contingency-filtered-table.qza
--o-visualization reads.qzv
And the error: There was an issue with viewing the artifact sample-contingency-filtered-table.qza as QIIME 2 Metadata:
Metadata must contain at least one ID.
Hi @annsantos!
This means that sample-contingency-filtered-table.qza
is empty, which means that your filtering step remove all features from the table.
What is the semantic type of table-no-mitochondria.qza
? (You can run qiime tools peek table-no-mitochondria.qza
). What @jwdebelius is suggesting above is to use a FeatureData[Taxonomy]
Artifact there, but it looks like you might be using a FeatureTable[Frequency]
Artifact.
Hi @thermokarst,
I run the qiime tools peek table-no-mitochondria.qza
My table-no-mitochondria.qza is from this filter:
qiime taxa filter-table
--i-table table.qza
--i-taxonomy taxonomy.qza
--p-exclude mitochondria
--o-filtered-table table-no-mitochondria.qza
So how can i filter mitochondria and have as output an featureData taxonomy?
In addition to my last comment, by contingency file cannot be empty because my i did a barplot with my table-no-mitochondria and it worked.
So how can i filter mitochondria and have as output an featureData taxonomy?
I think this is where the issue is, you should just tabulate the table-no-mitochondria.qza
file.
qiime metadata tabulate \
--m-input-file table-no-mitochondria.qza \
--o-visualization reads.qzv
Taking a step back, instead of running metadata tabulate
, it would make a lot more sense for you to run feature-table summarize
on this filtered table --- this visualizer is purpose-built for this type of data.
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