Editing metadata in a .qza file

[mshelomi (Matan Shelomi)]

I have demultiplexed, quality controlled, aligned sequences as single .fastq and single .fna files for each sample. I want to use QIIME2 for diversity and taxonomic analysis only.

Importing the .fna files with the following command

qiime tools import --type ‘SampleData[Sequences]’ --output-path outfile.qza --input-path manifest.csv --source-format SingleEndFastqManifestPhred33

I have an associated metadata.yml file. However, I see no way to incorporate it into data that is already demultiplexed. If I open the .qza file with an editor [TextWarngler], I see a metadata.yaml as follows:

uuid: 9fb71406-2bd4-404a-a11d-8ef73805f8e6
type: SampleData[SequencesWithQuality]
format: SingleLanePerSampleSingleEndFastqDirFmt

I want to replace this with my actual metadata.yaml file. TextWrangler won’t let me edit this. What should I do?

[thermokarst (Matthew Ryan Dillon)]

Hi there @mshelomi!

I want to replace this with my actual metadata.yaml file. TextWrangler won’t let me edit this. What should I do?

Please see this quote from @Mehrbod_Estaki, from your last topic on this forum:

Unknown input file format

The metadata file which provides environmental information about your samples is not required at the import step. Instead it is provided separately downstream as needed, depending on the analysis you are looking to do. More details, including its formatting and validation are explained here.

Specifically, the link to the metadata guide at the bottom. In general though I would recommend you take a step back and review the documentation and tutorials we have put together at docs.qiime2.org — the fundamental ideas behind QIIME 2 are described in great detail there, and will hopefully steer you in the right direction, generally speaking. As always, we are here to help!

Thanks!