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

Glossary
WFA A Workflow Analysis (WFA) run analyzes a quadrant of a slide that
undergoes a single ligation cycle. The quadrant contains beads
deposited at a lower density than the density of beads deposited for a
sequencing run. You can optimize sequencing results by performing
workflow analysis (WFA) runs.
Zero and One
Indexing
A WFA run determines the:
Applied Biosystems SOLiD 4 System SETS Software User Guide
Optimal library concentration: The library concentration for
optimal preparation of templated beads using the library. You
use this library concentration for any preparation of templated
beads for that library when the scale of templated bead
preparation is the same.
Bead enrichment efficiency: The proportion of beads that have
been successfully amplified using emulsion PCR (ePCR) as a
fraction of the total number of beads prepared. You use this
value to more accurately deposit successfully amplified beads
for a sequencing run.
WFA runs require the same materials as those materials needed for
sequencing runs. If you perform multiple WFA runs routinely, order
additional SOLiD Instrument Buffer Kits.
For preprocessed data, the first color space call is position 1, which
refers to the transition between the last base of the adapter and the first
base of the read. For processed data, the positions are 0-based so that
the first position (the prepended base) is 0 on both strands. The n th
position of the tag is numbered (n −1) in the forward direction and –
(n −1) in the reverse direction.
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