Hi, have you solved the problem? I have the similar problem with you. We also sequenced with Ion S5 SE600 platform. The company only gave us the demultiplex sequences file in .fna. I don’t know how to begin to create a manifest and metadata file to analyze by qiime2.
Hi @jmhuang,
You need to create them yourself. The data importing tutorial walks you through what’s required for your manifest.
Your metadata should have been collected when you collected your samples. It’s the clincial/site/sample information that gives context to your microbiome samples. You simply arrange it in a tabular file where each sample is a row. You can do this in excel, or if you have your data in another format (stata, sas, etc), you can also export these to a similar text file. The metadata tutorial goes over the formatting specifications.
Best,
Justine
Got it. I’ll try that. Thank you so much.
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Hi, Justine, I created a manifest and metadata table. And I have read the tutorial again. However, I still don't know how to start my work. My data was a fna file like this
The provider told me it's clean data with demultiplexing sequences. Could you help me with this? Thanks
Best regards,
Huang Jumin
Hi @jmhuang,
Do these correspond to a single file per sample?
Did they provide a counts table which corresponds to the sequences?
Do you know what was done to the data prior to its arrival? Did someone already do quality filtering on it?
Best,
Justine
Hi, Justine,
Each sample was in a file and there was a quality control table for these samples. I don’t know how they dealt with these data. The provider won’t supply us the barcode information and just told us we could analyze the data from clean data.
Best,
Huang Jumin
I think there’s an example of how to handle this data in the otu clustering tutorial, and a little bit more about the import here
I would still ask for fastq. Demultiplexed is okay, they don’t need to give you the barcodes, but per-basepair quality scores shouldn’t be unreasonable.
Best,
Justine
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Hi, Justine,
I have try again with your suggestion. And I found the following instruction.
Unfortunately, my data was one sample one file. So maybe I couldn't use qiime2 to analyze it. Thank you so much.
Best regards,
Huang Jumin
Hi @jmhuang,
If its otherwise correctly formatted, you could concatenate the files (I think cat works although @thermokarst or @Nicholas_Bokulich work bash wizardry that is beyond me. 
)
Otherwise, if you could also import after you build your table, as a secondary option.
Best,
Justine
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