GS Sequencer Output

3. GS Sequencer : 3.6 GS Sequencer Output

3.6	GS Sequencer Output

The files generated by the GS Sequencer application are called data sets and are placed in a Run directory (‘R_...’; see Note below), within the data partition of the instrument’s file system. The location of this data directory is set by the operating system environment variable $RIGDATA. The $RIGDATA setting is typically set to ‘/data’. The Run data sets include Run and image set information in the dataRunParams.parse file, and the set of raw images (*.png format, in the ‘rawImages’ sub-folder). When data processing is configured as part of the sequencing Run, additional data processing data set files are output. These are described in the GS Run Processor section of this manual (Part B, Section 1). The output files from the GS Sequencer application are described below.

•	dataRunParams.parse – This file is required in order to perform the image processing step of data processing. It contains all the parameters for the sequencing Run.

•	runComments.xml – This file contains the Run and region comments that were entered by the Operator as part of the sequencing Run setup (see Section 3.3.2, step 9).

•	imageLog.parse – This file is also required in order to perform the image processing step of data processing. It is a log file of all the images of the data set, including the reagent that was being flowed during the capture of each image.

•	*.png files - These files are required in order to perform the image processing step of data processing. They are the raw image files, showing photon counts for each pixel (in a rawImages sub-folder).

The following files are generated for troubleshooting purposes. While not strictly required for further analysis, it is recommended that these be archived with the raw data. You may be asked for these files if you seek help from Roche Customer Support (see Section 3.7.4) to resolve problems with a data set.

•	ptpImage.png

•	runlog.parse

•

•	*.icl (name of the script used during the sequencing Run or other procedure)

•	calParams.tgz

Full Run name: Run directory names (R_ …) are formed by appending the Run name entered during Run set up (see section 3.3.2, step 3) to information provided by the system, in the following format:

R_yyyy_mm_dd_hh_min_sec_machineName_OperatorID_RunName

The ‘R_’ denotes this as a Run directory, ‘yyyy_mm_dd_hh_min_sec’ is the timestamp for the beginning of the Run, ‘machineName’ identifies the GS FLX+ Instrument on which the sequencing Run is performed, ‘OperatorID’ identifies the Operator of the sequencing Run, and the ‘Run name’ entered during Run set up.

Some useful information that may be included in the Run name may include the PTP device size and ID (bar code number), the gasket type, the sequencing kit lot #, the genome being sequenced, and a Run number (e.g., ‘70X75_123456_2pad_060209_ecoli_Run3’). Spaces should not be used in the Run names – upper and lowercase letters and underscores are a good way to distinguish words.

If any data processing was carried out on this Run, a D_ directory is created within its R_ directory. Since a data set can be processed multiple times, an R_ directory can contain multiple D_ directories. See the General Overview section of this manual for more details.