Hello,
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!