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

Load a Reference Sequence
Specify a New
Reference
Applied Biosystems SOLiD 4 System SETS Software User Guide
Chapter 2 Prepare Run Settings
Load a Reference Sequence 2
If a specific reference sequence is not in the Reference Genome
drop-down list (Secondary Analysis Settings view), you can load a
new reference sequence before you start a run. Open the SETS
software and perform steps 1 to 4 below to add a new reference
sequence name to the list of choices you see in SETS.
Secondary analysis (sequence data alignments to a reference
sequence) would not occur without a preloaded reference sequence.
IMPORTANT! For more complex genomes (such as the human
genome), barcoded samples, and larger reference (and reads) the
secondary analysis should be performed off-instrument with the
BioScope Software. Refer to BioScope Software for Scientists
Guide: Data Analysis Methods and Interpretation (PN 4448431).
If a sample contains more than the maximum allowable number of
reads, the SETS software selects only up to the maximum allowed
number of reads and the rest will not be included in the results of the
secondary analysis.
IMPORTANT! Do not install BioScope Software on the SOLiD 4
Analyzer.
The Secondary analysis (sequence data alignments to a reference
sequence) will not occur without a preloaded reference sequence.
Perform secondary and tertiary analysis with the BioScope
Software. See “Load a Reference Sequence” on page 37.
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