Peak Identification tool
You use the Peak Identification tool to identify a list of regions that satisfy the coverage level requirements to be identified as a peak for any alignment project. This includes applications such as ChIP-Seq and or miRNA detection (where you want to locate highly covered regions) as well as any other application where you want to determine the location of regions that occur above a set threshold.
 | When “ChIP-Seq” is selected as the Application Type, automatic peak detection is applied during the initial processing and peak regions are indicated with brown ticks in the NextGENe Alignment viewer upon project completion. After automatic peak detection, you can then open the Peak Identification tool and manually specify settings for peak identification as needed. |
 | You can also use the Peak Identification tool to create a reference sequence. See Specialized Applications. |
You can specify that the software automatically identifies such regions, or you can manually set the values for identification.
Manual Setting | Description |
|---|---|
Coverage | The coverage threshold for a position to be considered part of a peak. Note: Although you can set the coverage level to any value, for ChIP-Seq or miRNA analysis, SoftGenetics recommends a value that is equal to twice the average coverage that is reported in statinfo.txt file. |
Gap | Maximum number of bases between regions that meet the coverage threshold to be considered one continuous peak. |
Set Baseline Noise | Used in conjunction with the Gap size to determine whether two nearby regions each with a coverage that is above the Coverage threshold are to be merged into one peak, or whether they are to remain as two separate peaks. • If the regions are separated by a distance that is less than the Gap size and the coverage in this region exceeds the Set Baseline Noise, then the two nearby regions are merged into a single peak. • If the regions are separated by a distance that is less than the Gap size but the coverage in this region does not exceed the Set Baseline Noise, then the two nearby regions remain separated. |
After the peaks have been identified in your data, a Peak Identification report is automatically generated. See Peak Identification report.