Input files
Input files for sequencing
The following table lists the input files for Bases2Fastq™. Bases2Fastq only uses the alignment file when the run manifest setting SpikeInAsUnassigned is set to True.
| File | Directory and File Name | Description | Quantity |
|---|---|---|---|
| Alignment | Root/Alignment/{read}_{tile}.aln | Binary files that indicate which polonies align to the PhiX Control Library | One per tile per read |
| Bases | Root/BaseCalls/{read}_C{cycle:000}.zip | Binary files that contain base calls and the associated Q scores | One per read and cycle |
| Filter | Root/Filter/{tile}.filter | Binary files that contain the filter status for each polony | One per tile |
| Location | Root/Location/{tile}.loc | Binary files that identify polony locations on the flow cell | One per tile |
| Run manifest, CSV | Root/RunManifest.csv | CSV file that records biological sample information and analysis settings | One per run |
| Run manifest, JSON | Root/RunManifest.json | JSON file that is reserved for Element processes | One per run |
| Run parameters | Root/RunParameters.json | JSON file that records information about the run configuration | One per run |
Input files for cytoprofiling
The following table lists the input files for Bases2Fastq. The target cell assignment manifest is required only when a --per-target-fastq optional argument is run.
| File | Directory and File Name | Description | Quantity |
|---|---|---|---|
| Bases | Root/BaseCalls/{read}_C{cycle:000}.zip | Binary files that contain base calls and associated Q scores | One per read and cycle |
| Filter | Root/Filter/{tile}.filter | Binary files that contain the filter status for each polony | One per tile |
| Location | Root/Location/{tile}.loc | Binary files that identify the polony locations on the flow cell | One per tile |
| Run manifest, CSV | Root/RunManifest.csv | CSV file that records biological sample information and analysis settings | One per run |
| Run manifest, JSON | Root/RunManifest.json | JSON file that is reserved for Element processes | One per run |
| Run Parameters | Root/RunParameters.json | JSON file that records information about the run configuration | One per run |
| Target Cell Assignment manifest, CSV | Root/TargetCellAssignment.csv | (Optional) CSV file that records target information | One per run |
| Target Cell Assignment manifest, JSON | Root/TargetCellAssignment.json | (Optional) JSON file that is reserved for Element processes | One per run |