Creating manifest file for fastq files that contain both forward and reverse reads

My .fastq files contain both forward and reverse reads in the same file. The manifest requires specification of forward or reverse reads:

sample-1,$PWD/some/filepath/sample1_R1.fastq.gz,forward
sample-2,$PWD/some/filepath/sample2_R1.fastq.gz,forward
sample-1,$PWD/some/filepath/sample1_R2.fastq.gz,reverse
sample-2,$PWD/some/filepath/sample2_R2.fastq.gz,reverse

Is there a way to use these files that have both or do they need to be separated?

Hello Kristin,

Great question!

Based on this answer, it looks like interleaved fastq files are not supported quite yet.

That issue is still open :frowning:

Let’s see if the Qiime developers can suggest a workaround.

Colin

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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