The Simple Peak Finder is based on the peak detection algorithm (Johnson, et al.,2007). This algorithm uses a sliding window to search for a specified number of reads within a region of specified length. If a peak is found, it is extended as long as there are reads within the window width.
The Simple Peak Finder reports the number of reads within the peak as the score for that peak. It also reports the start and end position for each peak and the position of the highest point within the peak. These can be accessed through the "Start", "End", and "Pinnacle" annotation values in the Peak Table after processing the data.
If you choose Simple Peak Finder as the peak detection method, the following options will be available:
•The Minimum number of reads within the region value defines how many reads that must be found within a region to call that region a peak.
•The Maximum distance between reads in the region value defines the width of the window the reads must be within to be considered for a given peak.
•The Minimum fold enrichment over the control option is enabled if a control lane has been specified. Peaks are only reported if the number of reads in the peak region of the treatment data are at least this many times greater than the number of reads in the peak region of the control data.
Note: Control data can only be used for ChIP-Seq experiments and is disabled for miRNA projects. You may specify control experiments in the Create Binding Proteins dialog of the Project Setup Wizard.
•The simple peak detection algorithm only considers the start location of each read and assumes all reads are the same length, which is equal to the Tag size. By default, QSeq will Automatically calculate tag size by taking the average read length and using this value in the Simple Peak Finder algorithm. You may uncheck this option and set the Tag size manually.