The Peak calling task is used to detect enriched genomic regions on reads generated from nucleic acid enrichment experiments such as ChIP-seq, DNase-seq, and MeDIP-seq. experiments. Partek^® Flow^® provides the widely used method of MACS2-model-based analysis¹ (http://liulab.dfci.harvard.edu/MACS/) to find peaks. It can be performed with or without control sample.

MACS2 dialog

Selecting MACS2 from the context sensitive menu will bring up the MACS2 task dialog. The interface will appear differently depending on the input aligned data node and whether there are sample attributes available in the Data tab.

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Peaks report

In the task report, each pair will generate a list of peaks displayed in a table (Figure 6). Use the drop down menu next to Peaks detected for... to select the pair.

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Click the Download button at the lower-right corner to download the peaks in a text file.

References

1. Zhang Y, Liu T, et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.

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