Importing Zymo fastq files

I just got data back from Zymo and was trying to process it through Qiime on my own. I'm having trouble successfully importing the data using PairedEndFastqManifestPhred33V2. Do you have any experience importing Zymo fastq files into Qiime?

Hello @Riley_doyle,

Can you provide some screenshots or an explanation of the structure of your data, and explain any steps that you've tried already to import your sequences? Have you read the importing docs?

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I have forward and reverse reads of three samples. Attached is what the fastq files look like.
Yes, I read the importing docs. It doesn't look like they follow the EMP protocol, or the Casava 1.8 format. That's why I tried to import the data with a manifest using PairedEndFastqManifestPhred33V2. However, when I did that, my quality plot looked like weird. (attached also)

Hi @Riley_doyle,
It looks like you do have data that should be imported using PairedEndFastqManifestPhred33V2.
Can you share your command you ran and a screenshot of your manifest?

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here the code I ran and a screenshot of my manifest as a txt file. Note: I changed files names

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path /home/rileykd/Qiime files/manifest.tsv
--output-path demux_seqs.qza
--input-format PairedEndFastqManifestPhred33V2

Hi @Riley_doyle
What error are you getting?

I'm not getting an error; my quality plots just look weird see above in my original post.

Your quality plots look weird because they were sequenced with NovaSeq or similar machine. They are binning quality scores, which results in such plots.
There were some concerns about how Dada2 would process such reads. However, according to Dada2 developers, it should handle it just fine. I think among all datasets I processed, 70% had such quality plots.


How do I move forward then?

Hello @Riley_doyle,

You can use dada2.

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The same way as usual. Dada2 or Deblur for denoising