My .fastq files contain both forward and reverse reads in the same file. The manifest requires specification of forward or reverse reads:
Is there a way to use these files that have both or do they need to be separated?
Based on this answer, it looks like interleaved fastq files are not supported quite yet.
That issue is still open
Let’s see if the Qiime developers can suggest a workaround.
I don’t have any progress to report on this, sorry. But I have added another cross-reference on our issue tracker. Thanks for letting us know you need this!
In the meanwhile you will need to use another program to demultiplex (like QIIME 1’s extract_reads_from_interleaved_file.py and then using
qiime demux emp-paired or similiar).
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