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

D
Appendix D Advanced Topic: Primary Analysis
Primary analysis overview
Primary analysis overview
Table 4 lists the stages in primary analysis, their inputs, and their
outputs.
Table 4 Primary analysis stages, inputs, and outputs
Analysis stage Inputs Outputs Steps
postBeadFinding
Primary
postScanSlide
Primary
postPrimerSet
Primary
Focal map and
first ligation
cycle “.tiff”
images
.tiff images
from each
ligation cycle
Focal map
“.tiff” images
Bead location (in
".spch" files)
Image statistics and
metrics (in
*_FOCALMAP_sum
mary.tab files)
Intensities, Color
calls, Quality
metrics, QV, in
".spch" files
Satay “.png” files
Summary data (tab)
Run status info
(traffic lights) (tab).
All ".spch" files Color-space raw
reads (“.csfasta”)
QV (“.qual”)
Reads statistics file
(“.stats” file).
For each panel, analyze the focal
map and first ligation cycle images
to identify beads.
1. Align images.
2. Extract intensities.
3. Classify colors (color calls).
4. Calculate quality value (QV).
5. Generate satay images.
6. Accumulate run status
information.
1. Assemble color-space reads
per panel.
2. Concatenate per-panel reads
into one single “.csfasta” file
(optional).
3. Filter reads shorter than
specified read length or
duplicate reads (optional).
162 Applied Biosystems SOLiD 4 System SETS Software User Guide