Where to Start from with R1 and R2 files

Hello Colleagues

From sequencing facility, I am provided with R1.FASTQ and R2.FASTQ via bacespacer.
Tutorial just tells how to download or import files and then do demultiplexing and quality filtration on those given files in .QZA QZA formate

Please tell how we can proceed with 2 fastq files provided
Note: I have already done this analysis on QIMME1 but now want to do on QIIME2

Hi @drmusk,

I typically get my sequences in R1.fastq and R2.fatsq from my illumina sequence facility as well. Check out this post. Let us know if this doesn’t answer your question.


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QIIME 2 2017.12 has a new cutadapt plugin which provides demux-single and demux-paired for demultiplexing reads where the barcodes are included within your reads!