Transcript report
By default, when the Transcript report first opens in the NextGENe viewer, it is displayed on the right side of the opened NextGENe viewer. You can click the Switch Report Layout icon on the NextGENe Viewer toolbar to select the location for showing the report (to the right or at the bottom of the NextGENe Viewer), or to elect to show only the report (the Alignment viewer is hidden), or to hide the report.
Field | Description |
|---|---|
Each entry (record) in the Transcript report represents a region or a link. Purple text indicates an annotated record and blue text indicates a novel record. | |
Index | The numerical value that NextGENe assigns to the record. |
Chr | The name of the chromosome where the record occurs. |
Start | The base number that indicates where the record starts. |
End | The base number that indicates where the record ends. |
Length | The length (in base pairs) for the region, or the length between the two ends of a link. N/A is displayed for fusion links. |
Gene | The name of the gene where the record is found. |
Exon(s) | One exon number is displayed in this column if the record is a region. Two exon numbers are displayed in this column if the record is a link. N/A is displayed in this column if there is not an annotated exon for the record. |
Link Number | Applicable only for link records. The number of reads that covered the link. Displays N/A for region records. |
PE Link Number | Applicable only for link records in paired end data. The number of pairs where one read maps to either end of the link. Displays N/A for region records and non-paired end data. |
Avg Coverage | Applicable only for region records. The average coverage of the region. N/A is displayed for link records. |
<-Coverage ->Coverage | Applicable only for link records. Average coverage of the regions that are linked. N/A is displayed for region records. |
Type | The type of region or link. |
Isoform | The NCBI accession number for the mRNA isoform. |
Protein | The NCBI accession number for the protein. |
Contig | The contig (region of the reference) where the record is found. |
Note: You can click any NCBI accession number to go to the NCBI website | |
The report is interactive:
Option | Description |
|---|---|
View records for only a specific chromosome and/or gene | By default, when the report is first generated, it displays all records for all chromosomes and all genes. You can select a chromosome on the Chr dropdown list and/or a gene on the Gene dropdown list. |
Dynamically update the display in the NextGENe viewer, | Double-click any variant entry in the report. |
Import the gene for a variant into Pathway Studio and visualize the biological pathway information for the gene | If you have a subscription to Pathway Studio, then you can right-click the variant, and on the context menu that opens, select View in Pathway Studio. Note: Before you can use the Paired Reads report in conjunction with Pathway Studio, your Pathway Studio access option must be set for the NextGENe Viewer. See Process menu (NextGENe Viewer main menu) in NextGENe Viewer main menu. |
Specify the information that is to be displayed in the report | On the NextGENe Viewer toolbar, click the Report Settings icon  . See Transcript report settings. |
Save the report to a text file | On the Reports menu, click Transcript Report > Save Transcript report. A default name (<project_name>_TransReport) and location (the project output folder) are provided, but you can change one or both of these values. |