Notification Codes and Troubleshooting
Notification codes indicate problems with the selected regions or targets. The following notification codes appear in the Design Warnings column of several DesignStudio tables for the three assays.
|
Code |
Description |
Assays |
Troubleshooting |
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AMRS |
Above Maximum Region Size. The target size exceeds the maximum. The maximum allowed regions sizes are:
|
|
Keep target lengths within allowable limits. |
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CB |
Cross-Binding. Cross-binding results from interaction between probes in the pool. |
TruSeq Targeted RNA |
Remove at least one assay from the cross-binding group. |
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D |
Duplicate target or region. The project contains duplicate targets. Homologous regions or merged targets can also cause duplications. |
|
Remove at least one assay from the duplicate group. |
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DP |
Duplicate Probe. |
TruSeq Targeted RNA |
Remove at least one assay from the duplicate group. |
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|
Low Spef |
The best probes found for this target are not unique in the genome. |
Enrichment |
This notification does not indicate that the design cannot work. However, you can try to resolve the problem using any of the following methods.
However, increasing density in a difficult region can increase the number of probes that have this warning. |
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N |
Undesignable sequence containing Ns or assembly gaps. |
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Check reference genome for Ns or gaps. Make sure that target coordinates do not include these features. |
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NT |
No transcript items found for this query. |
|
Check the targeting options to make sure that the proper value was selected. This error is most commonly seen when a coordinate range is used, but Exon Only is selected. Exons might not exist in that coordinate range. Check the spelling of the Transcript/Gene/rsID because a typo can result in this error. |
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Poor GC |
The best probes found for this target are high in GC content. |
Enrichment |
To remedy this, remove problematic targets, try to design around those areas in which those probes are found, or increase density to try to get better coverage. However, increasing density in a difficult region can increase the number of probes that would have this warning. This warning does not necessarily mean that the design will not work. |
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Targets will be merged |
Targets are within one amplicon length of each other. They are merged and designed as one contiguous region. |
TruSeq Targeted Amplicon |
This notification does not prevent designing the project. If you want separate targets, make sure that the coordinates are more than one amplicon length away from each other. |
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U |
Undesignable. The software cannot design the target. |
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Change design options such as Avoid SNPs, Dye, or Density. Expand the coordinate range of the desired region. If a particular exon has difficulty designing, reenter that exon with expanded coordinates through the Coordinates tab or file upload. |