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Input Files

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.

FileDirectory and File NameDescriptionQuantity
AlignmentRoot/Alignment/{read}_{tile}.alnBinary files that indicate which polonies align to PhiX Control LibraryOne per tile per read
BasesRoot/BaseCalls/{read}_C{cycle:000}.zipBinary files that contain base calls and associated Q-scoresOne per read and cycle
FilterRoot/Filter/{tile}.filterBinary files that contain the filter status for each polonyOne per tile
LocationRoot/Location/{tile}.locBinary files that identify polony locations on the flow cellOne per tile
Run manifest, CSVRoot/RunManifest.csvCSV file that records biological sample information and analysis settingsOne per run
Run manifest, JSONRoot/RunManifest.jsonJavaScript Object Notation (JSON) file reserved for Element processesOne per run
Run parametersRoot/RunParameters.jsonJSON file that records information about the run configurationOne per run