The G4 Sequencing Platform will output a number of files to your designated output location for each flow cell. Here is description of commonly used files.
- The “demux_filtered_fastqs” directory contains the FASTQ files that have been demultiplexed using the samplesheet associated with the run. If the demultiplexing was successful, a “demux_complete.txt” file should be created. If there is not a valid samplesheet, the output FASTQ files will be filtered to remove PhiX reads and bases with Qscore < 10 will be N-masked.
- The “unfiltered_fastqs” directory contains the lane level FASTQ files for each flowcell before demultiplexing, PhiX read removal, and base quality masking. This is the most raw/primitive sequence data output from the G4 sequencer. These are the files to use if you would like to demultiplex your data manually.
- Reporting files:
- A file named “run_complete.txt” should be in the folder if the sequencing run was completed successfully.
- A file named “demux_complete.txt” should be in the folder if the demultiplexing step was completed successfully.
- A file named “transfer_complete.txt” should be in the folder if the data transfer was completed successfully.
- Metric files: successful demultiplexing should also generate a number of metric files (with metric in the name) that can be used to determine how well the fastq data was demultiplexed.
See also the topic Run Folder in the G4 Sequencing Platform User Guide.