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

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

If the selected aligned data node was imported, the reference assembly used during data alignment needs to be specified.  Choose Choose the Assembly from the drop-down list within the MACS2 dialogue (Figure 1).  If If the selected lianged ata node was generated by Partek Flow, this option will not appear.

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In the Define pairs section, the left panel list all the sample names, add one pair at a time, select ChIP sample to put in  IP IP panel on the top-right, choose control sample to put in the Control panel on the bottom-right   (Figure 1). If there is no control sample in the experiment, the Control panel can be blank. If more than one ChIP or Control samples added, the samples will be combined (or pooled) in the analysis. 

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1. Zhang Y, Liu T, et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol.   20082008;9(9):R137.