Feed metadata and primer sequences into Qiime2 when sequences are already demultiplexed

Dear Qiime community and forum maintainers,

I am here contacting you with a request similra to the discussion from Merging paired end sequences after importing fastq manifest data. I have worked with Qiime 1.9, and only now start using Qiime 2 (installed 3 days 15.11.2017

My questions are below this following block and here is what I did:

  1. I downloaded demultiplexed (i.e. one file per sample) forward and reverse .fastq files from Illumina basespace.

  2. I created a manifest file called 05_manifest.txt (13.6 KB) which seemingly won't hold more then the three required metadata columns.

  3. I called qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path "$trpth"/"$inpth" --output-path "$trpth"/"$otpth" --source-format PairedEndFastqManifestPhred33 which worked fine.

  4. As my samples are already demultiplexed I called, as suggested in referenced thread, qiime demux summarize --i-data "$trpth"/"$inpth" --o-visualization "$trpth"/"$otpth" which worked fine.

I would be happy if you could assist with the following questions:

  1. How do I remove adapter sequences and primers, if I am skipping the demultiplex step? I am assuming they would still be in there.
  2. How can I feed my sample metadata information (a.k.a "mapping file" contents) "into Qiime", if this is normally done also at the demux step.

I would be looking forward to hearing from you in due course. I have screened other replies but could not find any answers specific to this question.

System versions
Python version: 3.5.4
QIIME 2 release: 2017.10
QIIME 2 version: 2017.10.0
q2cli version: 2017.10.0

Hi @Paul_Czechowski! Thanks for the detailed post, it made it really easy for us to follow what you are working on! :tada:

Have you had a chance to peek at this forum topic? Ultimately, the fastq manifest file is a completely different beast from the sample or feature metadata file.

If you haven’t had a chance to work through the tutorials, I strongly suggest you start here, before diving in to your own analysis - the Q2 documentation covers a lot of ground!

We generally try and keep one topic per thread — if you still have questions about this after reviewing the documentation, and looking at previous posts on the forum, please post a new topic and we will be happy to assist!

Thanks! :t_rex:

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