Creating a Reference File with the Peak Identification tool
In addition to using the Peak Identification tool to identify a list of regions that satisfy the coverage level requirements to be identified as a peak, you can use the Peak Identification tool to save these regions of the genome as a reference file and use them as a reference sequence.
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. |
When you use the Peak Identification tool, the Peak Identification report contains information about all regions of the reference that meet the coverage requirements. After peak identification, the results of the alignment project are displayed in the NextGENe Viewer. Brown lines indicate the regions that meet the requirements to be considered a peak.
 | For detailed information about the columns that are displayed in the Peak Identification report, see Peak Identification tool. |
To save the report to a .fasta file, click the Save Report icon 
on the report toolbar. A default name and location are provided for the file, but you can change both of these values.
on the report toolbar. A default name and location are provided for the file, but you can change both of these values.