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

[kristiny (Kristin)]

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?

[colinbrislawn (Colin J Brislawn)]

Hello Kristin,

Great question!

My .fastq files contain both forward and reverse reads in the same file.

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

How do I import interleaved fastq files?

Thanks so much for all that information! I’ve created an issue to track this format. This corresponds to extract_reads_from_interleaved_file.py in QIIME 1, so there’s a fair chance we’ll have this in the next few months as we work towards feature-parity with QIIME 1.

That issue is still open

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

Colin

[ebolyen (Evan Bolyen)]

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).