The FASTQ files are saved by lane and read or index (if used), which is indicated in the filename. For example, Undetermined_S0_L003_R1.fastq.gz is the unfiltered FASTQ file for lane 3, read 1, while Undetermined_S0_L001_I2.fastq.gz is for lane 1, Index 2.

Figure 1 unfiltered_fastqs folder