Importing a multiplexed fastq file using EMP single end pipeline

Hi,
I am trying to analyze my microbiome data (I have a single end multiplexed samples in one fastq.qz file and then a separate file which contains the barcodes). I imported using the EMPsingle end pipeline. However, when I visualized my demux.qxv I get the following message.

Danger: Some of the PHRED quality values are out of range. This is likely because an incorrect PHRED offset was chosen on import of your raw data. You can learn how to choose your PHRED offset during import in the importing tutorial.

I have looked at the other suggested import method using SingleEndFastqManifestPhred64 format. However, after reading it sounds like my starting input file has to be a demultiplexed data.

Is there a way to convert my data to PHRED 33 using the EMPsingle pipeline?

1 Like

Oh but it is demultiplexed! You had to demux in order to run demux summarize. You could export that Artifact, then create a SingleEndFastqManifestPhred64 pointing to the freshly exported (and demuxed) data in order to get these data normalized. In fact, there is a "relative manifest" file in the export dir already with all the sample IDs and filenames, you can just fire that up in an editor and make the changes necessary for that to be a SingleEndFastqManifestPhred64 file (absolute filepaths, for example).

Give it a shot and let us know how it goes! :t_rex: :qiime2:

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