View the Oligonucleotide Sequence Coverage Map - BioPharma Finder Software - View the Oligonucleotide Sequence Coverage Map - BioPharma Finder Software - BioPharma Finder Software

Prerequisites

1. You have loaded the experiment results are viewing the Coverage page under the Mapping tab.

Procedure

1. In the Coverage Results table, select the row of an oligonucleotide, raw data file, or component.
1. If you select a row at the oligonucleotide (top) level, the Sequence Coverage Map displays the sequence coverage results for from the first (or only) raw data file in the experiment.
2. (For experiments with multiple raw data files) If you select a row at the raw data file (second) level, the Sequence Coverage Map displays the sequence coverage results from the specified raw data file.
3. If you select a row at the component (lowest) level, the Sequence Coverage Map still displays the sequence coverage results for the associated raw data file (see above).
4. The upper portion of the Oligonucleotide Sequence Coverage Map displays a table of oligonucleotides with coverage and abundance values. This table displays information from the Coverage Results table for each raw data file. Directly below this table, the application lists the parameters specified in the Coverage Map Options dialog box. For more information on these parameters, see Modify Oligonucleotide Sequence Coverage Map parameters.
5. The lower portion of the map displays the color-coded sequence coverage information for the oligonucleotide or raw data file selected in the Coverage Results table. The color-coding indicates the MS signal intensity of the predicted fragments. The application labels each nucleotide in the map with its retention time (RT) and color-codes the nucleotides by intensity with red, orange, yellow, green, cyan, blue, shades of gray, and white colors, showing red as most intense and white as least intense.

6. IMPORTANT

   The signal intensity-based color-coding displayed in the Oligonucleotide Sequence Coverage Map is not related to the customizable shading settings set for the Coverage chromatogram.

   For more information on the color-coding used in the Coverage chromatogram, see View the Coverage chromatogram.

7. You can specify which components to include in the Oligonucleotide Sequence Coverage Map. See Select Oligonucleotide Sequence Coverage Map components.
8. Additionally, you can modify the oligonucleotide recovery parameters and the number of nucleotides displayed per row on the Oligonucleotide Sequence Coverage Map. See Modify Oligonucleotide Sequence Coverage Map parameters.

9.