If you are following the ChIP-Seq or miRNA workflows, the Peak Detection Settings tab will be available. Choose one of the following peak detection algorithms from the Method drop-down menu:
•QSeq Peak Finder – This algorithm calculates peaks in a normalized reads-per-million space. The QSeq finder can do simple read shifting, handle repeated reads, and consider the directionality of the reads when calling peaks.
•Simple Peak Finder - This is a simple "sliding window" peak detection algorithm that looks for a specified number of reads within a window of a specified length. If a peak is found, it is extended as long as there are reads within the window. Control data may be used to disqualify false peaks.
•MACS Peak Detection – The MACS, or Model-based Analysis of ChIP-Seq, algorithm assumes that a true binding site will be flanked by peaks of reads. MACS attempts to build a model of the distance between peaks and uses the model to shift reads in order to call a peak over the true binding site.
The available parameters and defaults will change based on which method you choose.