Importing demultiplexed fastq


I am working with a study that I started processing using Qiita. The deblur step is not completing on qiita because the study is too large (as confirmed by qiita help as it includes 9 miSeq sequencing lanes), so I am trying to pull the demultiplexed fastq file from the qiita study and import it into qiime2 for analysis on our server. However, I can’t find an appropriate import command.

  • The import tutorial only has options for demultiplexed fastq or per-sample fastq with a manifest. Neither of these describe the single fasq for the whole study that I have
  • I found this thread Importing seqs.fna that would help me import the fasta file from qiita, but I want to analyze using deblur, so I need the quality information in fastq

Is there an import method I am missing that would help me? The only alternative I know of is to download all of the original fastq files, demultiplex and deblur them individually, and then merge them, but that is a lot in a study this large.

Thank you!

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HI @aeriel.belk,
I am guessing the format is a qiime1-style demultiplexed file and does NOT have qual scores. If so, you can import as a SampleData[Sequences] artifact. However, that data type is not compatible with q2-deblur :disappointed:. At the moment, only OTU picking can accept this file type.

You can process with deblur outside of QIIME 2 and then import the outputs.

The other option would be to get access to the non-demultiplexed raw fastqs.

I hope that helps!

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