Applied Biosystems SOLiD™ 4 System SETS Software User Guide ...

D
Appendix D Advanced Topic: Primary Analysis
Primary analysis workflow
Perform primary re-analysis
To perform primary analysis manually, use the following
command:
jprimaryanalysis.sh –-ini=PrimaryParametesr.ini
Note: Only buildReads tasks are executed for re-analysis. Neither
beadFinding nor colorCalling are enabled for re-analysis in the
pipeline.
The PrimaryParameters.ini file can be found inside the JobID folder
with the file named parameters.ini.
$sampleJobFolder/postPrimerSetPrimary
To prepare for the re-analysis:
1. Create a new analysis directory, such as:
postPrimerSetPrimary.m1.
2. Copy the following file onto the new directory.
parameters.ini
3. Edit the following file to ensure that all the paths are correct.
PrimaryParameters.ini
4. Remove parameters marked for daemon property.
For example:
analysis.job.id
(Default behavior does not accept non-integer.)
update.solid.script
(Used by the daemon for updating the SOLiD 4 System
database.)
logging.socket
(Used by the daemon for logging analysis progress.)
5. Enter
jprimaryanalysis.sh --ini=PrimaryParameters.ini
170 Applied Biosystems SOLiD 4 System SETS Software User Guide