Peak Identification report
After you use the Peak Identification tool to identify the peaks in your data, a Peak Identification report is automatically generated. To view this report, on the NextGENe Viewer main menu, click Reports > Peak Identification Report. This report shows all the peaks that were detected across the entire reference sequence. If you are carrying out targeted sequencing and want to view the peaks for specific regions, then you can use the File > Load BED file option to load a BED file.
The report provides the following information:
Value | Description |
|---|---|
Chr | The chromosome on which the peak region was found. |
Reference Region | The beginning and ending bp for the region based on the overall reference position. |
Chromosome Region | The beginning and ending bp for the region based on the chromosome position. |
Length | The total length of the region in bp. |
Coverage | The 75th percentile of coverage for the region. |
Transcript Site | The central regions for peaks that are larger than 100 bp. Each peak end is trimmed by 7.5% of the region length, for a total of 15% of the region length. |
Gene Distance | The location of the peak relative to the nearest gene. • If a peak overlaps the start of a gene, then “Gene Distance” is listed as 0. • If it occurs before a gene, then it is a negative value measuring the distance between the peak and the start of the gene. • If it occurs within a gene, then it is a a positive value measuring the distance between the peak and the start of the gene. • If it is not located in a gene and the next start of a gene is more than 5,000 bp away, then the distance is listed as “None.” • The direction of genes is accounted for. For example, a peak is “before” a gene if it occurs at an earlier position than a forward gene or at a later position than a reverse gene. Only the closest gene is reported. |
Gene Direction | Not displayed by default. The strand (plus or minus) on which the gene is found. |
Read Orientation | Not displayed by default. The percentage of reads that aligned to the region in the forward direction / the percentage of reads that aligned to the region in the reverse direction. |
Sequence | The sequence for the peak region. |
The report is interactive:
• To save the report to a .fasta file, on the report toolbar, click the Save Report icon 
. A default name and location are provided for the file, but you can change both of these values.
. A default name and location are provided for the file, but you can change both of these values.• To modify the report settings, on the report menu, click Settings > Settings, or on the report toolbar, click the Settings icon 
to open the Peak Identification Settings dialog box, and then modify the report settings on the General tab or Display tab as appropriate. The report display is dynamically updated after you click OK to save the settings.
to open the Peak Identification Settings dialog box, and then modify the report settings on the General tab or Display tab as appropriate. The report display is dynamically updated after you click OK to save the settings.