DADA2 Feature ID to Rep-Seq Mapping

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Hello!

I would like to know which representative sequences from the rep-seq.qza file are from which one of my samples. That is, what ASVs were found where.
Does anyone know if there is a way to map the feature IDs in the rep-seq.qza file to the sample files?

Thank youuuu!
Taylor

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Hi @Taylorr ,
Good question. This is the information found in your feature table output by dada2. You can view this directly as a table by passing it as an input to qiime metadata tabulate, but a better way to visualize would be as a heatmaps (see qiime feature-table heatmap --help).

Good luck!

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Hey Nicholas!

The heat maps seems like a great idea! Thank you bring this to my attention. I have poked around in the documentation a bit and I think I'd like to generate a heat map visualization for my data - however, I am a bit confused about the --m-metadata-column parameter ... it seems like this really depends on the context of your interests (for instance, I saw one example where this parameter specified taxonomy classifications) and I am not sure what to use for it in order to generate a heat map with my own data.

I would be interested in your thoughts and insights on this!
Best,
Taylor

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definitely. these parameters are optional, so you do not need to use them. They are used specifically if you wish to label the samples or features by some metadata (e.g., to indicate which group a sample belongs to). But you do not need to use them if you don't have a relevant use case.

Good luck!

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Thank you for clarifying. I tried to run the command but ... it seems that the table.qza file is too large. This seems like an issue because I would like a fully representative heat map visualization. Have you ever dealt with the following error?

(qiime2-2022.2) FVFVV65QJ1WK:dada2-rerun taylorrayne$ qiime feature-table heatmap 
    --i-table table.qza     
    --o-visualization heatmap.qzv      

Plugin error from feature-table:

  Image size of 73885x7530 pixels is too large. It must be less than 2^16 in each direction.

Debug info has been saved to /var/folders/mz/jmj4s01d4c5gny718z25n8sw0000gq/T/qiime2-q2cli-err-wq2zhyyq.log
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Yes you are correct, the heatmap is too large to display. You have too many features in your feature table! You could filter out low-abundance features. If you really want to view all features, the only other option is to use qiime metadata tabulate to view as a searchable table.

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Thank you again for the help and advice!
I will tinker around :wink:

Taylor