Importing fastq multiplexed data without knowing anything about phred scores

Hi Qiime2 world,

I just got my first batch of MiSeq data and I spent a bunch of time reading the qiime2. org website, and I did all the tutorials. However, I’m having a hard time getting my own data into qiime2. I have paired-end multiplexed data. I do not have a separate file for each sample, instead I have one .fastq file ( not fastq.gz) for the forward reads, one for the reverse reads and one for the indexing barcodes. As far as I can tell, I don’t have any information on the quality (phred scores) of the sequences. Given this information can you advise me on which approach I should use to import my data. Any insights are much appreciated.

Hello @sgrove!


This sounds a lot like the EMP format, with the exception of your files not being gzipped (.gz).

Really? That would surprise me, since fastq is designed to have that kind of information (the quality is the “q” in fastq*) - how about you run the head command on your forward reads and copy-and-paste that information here?

head my-forward-reads.fastq

In the meantime, it sounds like you can probably gzip your files, and use the EMP paired-end import format. To gzip your files, you could run something like this:

gzip my-forward-reads.fastq
gzip my-reverse-reads.fastq
gzip my-barcodes.fastq

Then, rename them to match that format’s directory specification (detailed in the link above):

mv my-forward-reads.fastq.gz forward.fastq.gz
mv my-reverse-reads.fastq.gz reverse.fastq.gz
mv my-barcode-reads.fastq.gz barcodes.fastq.gz

Hopefully that helps get you moving - keep us posted if you get stuck! :t_rex:

Thank so much for you help! You’re right, my fastq files of course had quality data contained within. Zipping my files with the script you provided did the trick and got me started. Thanks so much!

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