If a project was provided in the sample sheet, then the FASTQ files are saved in sub-folder with the project name.
Figure 1 demux_filtered_fastqs folder
The FASTQ files are saved by sample, lane, and read, which is indicated in the filename. For example, SID123XYZ_rep1_S1_L001_R1.fastq.gz is the FASTQ file for SID123XYZ_rep1 in lane 1, read 1. The S1 indicates that this was the first sample in the sample sheet. If a FASTQ file is compiled from different lanes, the lane designator is set to L000 (for example, SID123XYZ_rep1_S1_L000_R1.fastq.gz).