Beckman Coulter CEQ 8000, User Manual

Page: 179 / 382

Quality Values
User’s Guide 165
• the average Call Score/Quality Value in a window of 25 bases falls below 0.75 -
0.8 on a linear scale and 6 - 7 on a log scale,
and
• there are at least 5 bases within that 25 base window whose Call Score/Quality
Value are less than 0.75 on a linear scale and 6 on a log scale.
Performing Quality-based Trimming
To setup Quality-based trimming, open the Sequence Analysis module and follow the
steps below.
1. Open a result and select the
Analysis | Working Analysis Parameters
menu
item.
2. Click the
Edit
button to open the Sequence Analysis Parameters Editor .
3. Select the Quality-based Trimming tab.
4. Select the
Ends To Be Trimmed
and the
Trimming Stringency
.
5. Click
Save As
and save the new parameters.
6. Click
OK
.
At this point, the result can be trimmed.
1. Select the
Analysis | Trim Based on Quality
menu item.
2. The Analysis Parameters, created in the steps above, should be listed. If not, click
Use Stored Parameters
and select the appropriate Analysis Parameter.
3. Click
OK
.
The resulting Base Sequence and Trace view displays the base letters, if poor quality,
as strikethrough after a Quality-based trim has been performed as shown in
Figure 100.
When performing Quality-based and Sequence-based trimming,
Quality-based trimming is always performed first.