Importing demultiplex paired end, what is manifest format?

I have raw data (without barcode and primer) run on Illumina paired-end platform looks like this:
- DMX12345_L1_SAMPLE1_1.fq.gz
- DMX12345_L1_SAMPLE1_2.fq.gz
- DMX12345_L1_SAMPLE2_1.fq.gz
- DMX12345_L1_SAMPLE2_2.fq.gz

As far as I understand, this file already demultipexed. So, I want to start with importing data and I used this command:

qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path casava-18-paired-end-demultiplexed
–source-format CasavaOneEightSingleLanePerSampleDirFmt
–output-path demux-paired-end.qza

Can I just rename the file name to be like this (below)? And then used the demux.qza to run DADA2?

_- SAMPLE1_L001_R1_001.fastq.gz _
- SAMPLE1_L001_R2_001.fastq.gz

I have looked at Importing data tutorial, but but still unclear about the manifest format, do I need to create it together with importing paired end demultiplexed data?

Thank you.

Hey there @eemannur!

You could certainly do that, but we have another alternative import method that will likely be less work! Check out the fastq manifest section of the importing guide for more detail!

Cool, so it looks like you saw that already! All the manifest is is a file with info about what files belong to what samples - you can write this in a text editor, or a spreadsheet program. When you “import” that manifest, the importer reads the contents of the file and says “okay, SAMPLE 1 is made up of /path/to/DMX12345_L1_SAMPLE1_1.fq.gz for the forward reads and DMX12345_L1_SAMPLE1_2.fq.gz for the reverse reads. :heavy_check_mark:

Make sense? Let us know how it goes! :t_rex: :qiime2:

Does this means in importing data, I can choose using manifest format or Casava 1.8?

In manifest format, I do not know whether to use phred-33 or phred-64. I have no idea about Illumina software version.


Probably 33 - unless your reads are pretty old. Check with your sequencing center if you need a hand there.

Hope that helps! :qiime2:

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Thank you very much @thermokarst

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