Preparing fastq files

Question

[rosypink160]

I am a bioinformatics noob who has just begun to learn. Can anybody suggest how do we create R1 and R2 files from A sample run and how to we know the no. of reads in the R1 and R2 files. This is for the workflow in DADA2

[rpolicastro]

The R1 and R2 fastq files are what you get from the Illumina sequencer if you did a paired end run, so it's a little unclear what you are starting with and what you want to accomplish.