Very glad you were able to work it out! Thank you for confirming!
I would like to ask also about the necessity of metadata file in command
qiime diversity core-metrics-phylogenetic.
My problem is … I don’t have metadata table, as my input to qiime is already demux (Illumina pair end sequences in fastq files).
I followed these tutorials
- to import pair end: https://docs.qiime2.org/2018.8/tutorials/importing/
- and to analyse: https://docs.qiime2.org/2018.8/tutorials/moving-pictures/#demultiplexing-sequences
In second tutorial, I remove option --m-metadata-file in all commands (DADA2 for example). I didn’t need it until diversity command. How can I follow?
Is there a command like:
Thanks in advance
This is answered above:
Sample metadata is used in many different commands — yes, for demux, but also for other steps. Because sample metadata can contain all sorts of information about samples!
You need to create your own metadata file from scratch. Check out the metadata files in the tutorials you are following to see some examples. Read here for a complete guide on formatting etc.
No, because only you know what metadata are associated with your samples. Again, check out the tutorials to see examples of what you might put in a metadata file.
Thanks for pointing me toward metadata page, I had already found it, but I was worried of manually writing the metadata. And also that I need BarcodeSequence and LinkerPrimerSequence columns, as there were in tutotial examples … and obviosly I don’t have them, since I import demux data.
I solved it by downloading TSV file from visualization of stats-dada2.qzv and altering the columns.
Unfortunately, yes — we have yet to devise a method to automatically compile metadata.
You do not need those columns.
The metadata format is completely flexible — columns are only used as needed, and there are (essentially) no requirements on what needs to be in there — the tutorial you’ve seen gives the few rules.
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