Inputs and Outputs

Input files for Bases2Fastq are the files output from a run. AVITI™ OS generates the input files and transfers them to a run folder in your storage location.

During an execution, Bases2Fastq generates an output folder that contains the output files, an info folder, and a Samples folder. The Samples folder organizes FASTQ files and sample metrics into one subfolder for each sample. If the run manifest for the execution uses projects, the Samples folder creates one subfolder for each sample per project.

Example Output Directories for Sequencing

With Project Folders

The following file structure is a example of an output directory when the run manifest groups samples into projects. Optional arguments can change the structure of output files.

output
├── 20230404-Bases2Fastq-Example-Run-QC.html
├── IndexAssignment.csv
├── Metrics.csv
├── RunManifest.csv
├── RunManifest.json
├── RunParameters.json
├── RunStats.json
├── Samples
│   ├── Project1 ... (for n projects)
│   │   ├── Project1_QC.html
│   │   ├── Project1_RunStats.json
│   │   ├── Project1_metrics.csv
│   │   ├── Project1_index_assignment.csv
│   │   ├── sample_0 ... (for n samples in the project)
│   │   │   ├── sample_0_R1.fastq.gz
│   │   │   ├── sample_0_R2.fastq.gz
│   │   │   └── sample_0_stats.json
│   ├── Project2
│   │   ├── Project2_QC.html
│   │   ├── Project2_RunStats.json
│   │   ├── Project2_metrics.csv
│   │   ├── Project2_index_assignment.csv
│   │   ├── sample_3 ... (for n samples in the project)
│   │   │   ├── sample_3_R1.fastq.gz
│   │   │   ├── sample_3_R2.fastq.gz
│   │   │   └── sample_3_stats.json
│   └── Unassigned
│       ├── Unassigned_R1.fastq.gz
│       └── Unassigned_R2.fastq.gz
├── UnassignedSequences.csv
└── info
    ├── RunManifestErrors.json
    └── bases2fastq.log

Without Project Folders

The following file structure is a example of an output directory without projects. Optional arguments can change the structure of output files.

output
├── 20230404-Bases2Fastq-Example-Run-QC.html
├── IndexAssignment.csv
├── Metrics.csv
├── RunManifest.csv
├── RunManifest.json
├── RunParameters.json
├── RunStats.json
├── Samples
│   ├── Unassigned
│   │   ├── Unassigned_R1.fastq.gz
│   │   └── Unassigned_R2.fastq.gz
│   ├── sample_0 ... (for n samples in the project)
│   │   ├── sample_0_R1.fastq.gz
│   │   ├── sample_0_R2.fastq.gz
│   │   └── sample_0_stats.json
│   ├── sample_1 ...
├── UnassignedSequences.csv
└── info
    ├── RunManifestErrors.json
    └── bases2fastq.log

With Grouped FASTQ Files

The following file structure is a example of an output directory when the execution uses the --group-fastq optional argument. Additional optional arguments can change the structure of output files.

output
├── 20230404-Bases2Fastq-Example-Run-QC.html
├── IndexAssignment.csv
├── Metrics.csv
├── RunManifest.csv
├── RunManifest.json
├── RunParameters.json
├── RunStats.json
├── Samples
│   ├── DefaultProject
│   │   ├── DefaultProject_IndexAssignment.csv
│   │   ├── DefaultProject_Metrics.csv
│   │   ├── DefaultProject_QC.html
│   │   ├── DefaultProject_RunStats.json
│   │   ├── sample_0_R1.fastq.gz ...(for n samples)
│   │   ├── sample_0_R2.fastq.gz ...(for n samples)
│   │   ├── sample_0_stats.json  ...(for n samples)
│   ├── Unassigned_R1.fastq.gz
│   └── Unassigned_R2.fastq.gz
├── UnassignedSequences.csv
└── info
    ├── RunManifestErrors.json
    └── bases2fastq.log

With Grouped FASTQ Files and No Projects

The following file structure is a example of an output directory when the execution uses the --group-fastq and --no-projects optional arguments. Additional optional arguments can change the structure of output files.

output
├── 20230404-Bases2Fastq-Example-Run-QC.html
├── IndexAssignment.csv
├── Metrics.csv
├── RunManifest.csv
├── RunManifest.json
├── RunParameters.json
├── RunStats.json
├── Samples
│   ├── sample_0_R1.fastq.gz ...(for n samples)
│   ├── sample_0_R2.fastq.gz ...(for n samples)
│   ├── sample_0_stats.json  ...(for n samples)
│   ├── Unassigned_R1.fastq.gz
│   └── Unassigned_R2.fastq.gz
├── UnassignedSequences.csv
└── info
    ├── RunManifestErrors.json
    └── bases2fastq.log

Example Input Directory for Sequencing

The following file structure is an example of an input directory for sequencing:

Example-Run-Directory
├── Alignment
│   └── L1R02C01S1
│       ├── R1_L1R01C01S1.aln
├── BaseCalls
│   └── L1R02C01S1 ...(for n tiles)
│       ├── I1_C001.zip ...(for n I1 cycles)
│       ├── I2_C001.zip ...(for n I2 cycles)
│       ├── R1_C001.zip ...(for n R1 cycles)
│       ├── R2_C001.zip ...(for n R2 cycles)
├── Filter
│   ├── L1R02C01S1.filter ...(for n tiles)
│   ├── L1R02C01S2.filter
├── Location
│   ├── L1R02C01S1.loc ...(for n tiles)
│   └── L1R02C01S2.loc
├── RunManifest.csv
├── RunManifest.json
└── RunParameters.json

Example Output Directories for Cytoprofiling

Per-batch (default)

output
├── info
│   └── Bases2Fastq.log
├── Samples
│   └── WellA1...(for n wells)
│       ├── A1_B01_R1.fastq.gz...(for n batches)
│       ├── A1_B02_R1.fastq.gz...(for n batches)
│       └── A1_B03_R1.fastq.gz...(for n batches)
│   └── WellA2...(for n wells)
│       ├── A2_B01_R1.fastq.gz...(for n batches)
│       ├── A2_B02_R1.fastq.gz...(for n batches)
│       └── A2_B03_R1.fastq.gz...(for n batches)
├── Panel.json
├── RunParameters.json
├── RunManifest.csv
├── RunManifest.json
├── TargetCellAssignmentManifest.csv
└── TargetCellAssignmentManifest.json

Per-target-mask

When you perform target to cell assignment with Teton Atlas™ chemistry, per-target-site FASTQ files are generated with independent target site masks. To trigger this, use the --per-target-fastq option combined with a Target Cell Assignment manifest that contains per-target basemasks.

output
├── info
│   └── Bases2Fastq.log
├── Samples
│   └── WellA1...(for n wells)
│       ├── TargetSite1_A1_B01_R1.fastq.gz...(for n TargetSites for n batches, including target to cell assignment)
│       └── A1_B02_R1.fastq.gz...(for n batches)
│   └── WellA2...(for n wells)
│       └── TargetSite2_A2_B01_R1.fastq.gz...(for n TargetSites for n batches, including target to cell assignment)
├── Panel.json
├── RunParameters.json
├── RunManifest.csv
├── RunManifest.json
├── TargetCellAssignmentManifest.csv
└── TargetCellAssignmentManifest.json

Example Input Directory for Cytoprofiling

input
├── BaseCalling
│   ├── BaseCalls
│   ├── CellXform
│   ├── Filter
│   └── Location
├── CellSegmentation
├── RunParameters.json
├── Panel.json
├── RunManifest.csv
├── RunManifest.json
├── TargetCellAssignmentManifest.csv
└── TargetCellAssignmentManifest.json