reads and taxonomy

annsantos · October 11, 2019, 2:43pm

Hi,

Anyone one knows if there is a way of knowing how much reads my principal taxa are responsible for?

Thank you

jwdebelius · September 26, 2019, 8:20am

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

annsantos · September 26, 2019, 10:35am

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.

jwdebelius · September 26, 2019, 11:33am

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

annsantos · September 26, 2019, 1:18pm

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.

thermokarst · September 26, 2019, 1:24pm

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.

annsantos · September 26, 2019, 2:15pm

Hi @thermokarst,

I run the qiime tools peek table-no-mitochondria.qza

UUID: f430fd1c-75d8-46aa-80af-460f998b655a
Type: FeatureTable[Frequency]
Data format: BIOMV210DirFmt

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?

annsantos · September 27, 2019, 10:50am

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?

thermokarst · October 1, 2019, 4:54pm

thermokarst · October 2, 2019, 11:33pm

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

thermokarst · October 2, 2019, 11:33pm

annsantos · October 8, 2019, 12:35pm

It didn’t work. Won’t open:

stays like this forever

thermokarst · October 11, 2019, 2:43pm

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.