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1. Overview of the 454 Sequencing System Software : 1.3 Data Output and Folder Structure
1.3
Data Output and Folder Structure
1.3.1 Data Acquisition (GS Sequencer and GS Junior Sequencer) Results: the Run Folder
1.3.2 Data Processing (GS Run Processor) Results: the Data Processing Folder
1.3.3 Data Analysis Applications Results
This section provides an overview of the listing and organization of the files that are generated at each step of data processing or data analysis, and made available to the user.
After a sequencing Run, results can be found in the “/data” directory on the GS FLX+ Instrument or the GS Junior Attendant PC, grouped by date, where each “date” folder contains individual Run folders. Each Run folder is identified by the Run name specified during Run set up (i.e. with an ‘R_’ prefix, denoting ‘R’un; see first “Note” below). Run folders contain the raw data of the sequencing Run (i.e. the results of the GS Sequencer or GS Junior Sequencer application), as well as any Data Processing folder(s) for that Run (identified by a ‘D_’ prefix, for ‘D’ata). Data Processing folders, in turn, contain the results of the image processing and/or signal processing steps.
 
”tmp” sub-directory required: The /data directory in the GS FLX+ Instrument on-instrument computer or the GS Junior Attendant PC contains a tmp sub-directory. Do not delete the tmp sub-directory as it is required for the proper functioning of the instrument software.
 
Because the data analysis applications are typically performed on a pool of sequencing Runs rather than on any single Run, their results are not associated with a specific sequencing Run or data processing invocation; rather, assembly, mapping and amplicon variant analysis results are deposited in the “current working directory” at the time the application is launched, or written to a directory specified by the user (see section 1.3.3). The SFF Tools commands also usually deposit their output into the “current working directory” or a directory specified on the command line.
 
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The user enters a unique name for the Run during set up. A good choice for a unique name could be structured as follows: “PicoTiterPlate device size and barcode #, kit lot #, genome, run #”; e.g. “70x75_123456_081708_ecoli_Run1”. To form the complete name of the Run files, the date stamp, time stamp, instrument name, and user name will be added automatically in front of this unique Run name. The name structure is:
 
“R_yyyy_mm_dd_hh_min_sec_machineName_userName_uniqueRunName”.
 
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Before running any data processing or data analysis application (GS Run Processor, GS De Novo Assembler, GS Reference Mapper, or GS Amplicon Variant Analyzer), the necessary input data for the sequencing Run(s) being processed or analyzed (see Table 1 and Table 2) must be made available to the DataRig or GS Junior Attendant PC where the application is located. The GS FLX+ Instrument or GS Junior Attendant PC can be configured to automatically transfer the output files that result from the GS Run Processor application to a remote disk or DataRig (see the section on data transfer scripts in the GS FLX+ System Site Preparation Guide or the GS Junior System SysAdmin Guide). Alternatively, the Data tab of the GS Sequencer application on the GS FLX+ Instrument, or of the GS Junior Sequencer application on the GS Junior Attendant PC, can be used to transfer the raw images of sequencing Run(s) to a pre-configured destination. For more information on the Data tab of the GS Junior Sequencer application, see Part A of this manual (Section 2 in the GS Junior System version or Section 3 in the GS FLX+ System version).