What Are Unfiltered FASTQ Files?

The unfiltered_fastqs folder in the Run Folder contains the FASTQ files before filtering or demultiplexing.

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

11/29/2023