what dose "S" mean in rowdata_file??

i receive row data form sequencing center..
file name is like this
C1.fastq.qz
C2.fastq.qz

but i know if i want import this file to qiime2 , i should change file name like this
C1_S12_L001_R1_001.fastq.gz
C2_S12_L001_R1_001.fastq.gz

but i don`t know "S12" number mean....what Lane number(L001)
It doesn't matter if I put in random(1~100) numbers?
and
It doesn't matter if I put in L001 at all sample??

Hi @svbreqwaiu01 ,

You do not need to change the names. QIIME 2 can accept multiple formats and what you are describing here is the CASAVA 1.8 format (which uses a file naming scheme that is created by Illumina).

Instead of giving your files arbitrary names to fit the CASAVA 1.8 format, you could also use the appropriate "manifest" format for your files (basically, provide a manifest file that links each sample ID to each filepath). The different manifest formats are described in the tutorial linked below.

You should check the Illumina website for more details, but a basic description is given here:
https://docs.qiime2.org/2022.2/tutorials/importing/#casava-1-8-single-end-demultiplexed-fastq

Good luck!

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thank you
i don`t know where is barcode seqeunce.
should i ask barcode sequence to NGS center??

No. QIIME 2 does not actually use that information, I believe it only grabs the sample ID. So you can just give an arbitrary label if you want to "fake" the Casava 1.8 format for the purpose of importing to QIIME 2.

But I really recommend just using the manifest format described in that tutorial, since you do not have the true Casava 1.8 format. Creating a manifest would be easier than "faking" Casava 1.8.

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