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 |