The 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 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.

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

The effective Effective genome size is the genome size of the regions that can be sequenced. Because of the repetitive features on the chromosomes, the actual mappable genome size will be smaller than the original size, typically about 70%-90% of the genome size. There are presets of 4 species based on MACS2 recommendation¹ for this parameter:

• hs – Homo sapiens, size is 2.7e9
• mm – Mus musculus, size is 1.87e9
• ce – Caenorhabditis elegans, size is 9e7
• dm – Drosophila melongaster, size is 1.2e8

When Other... is selected, a specific value of the effective genome size needs to be specified with bps as unit (Figure 2).

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For data where no sample attributes were specified, for instance there are only two samples, the peak detection pairs needs to be manually defined. In the example in Figure 1, in there only two samples. For the Define pairs section, the left panel lists all the sample names (chip and mock) .  Add one pair at a time by selecting the chip sample to put in the IP panel on the top-right, and selecting the mock sample in the Control panel on the bottom-right.

If there is no control sample in the experiment, the Control panel can be blank. If more than one ChIP or Control samples are added, the samples will be combined (or pooled) in the analysis. 

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For data where the sample attributes are defined (Figure 3), you will have an additional option to add pairs pairing or grouping based on the attributeattributes. Figure 3 shows an example data with 4 samples, 2 time points, and there is one IP sample and one Input sample in each time point.

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When running the MACS2 task, the default sample attributes will be to use sample attribute to add used to define the multiple pairs with a single mouse click (Figure 4). 

There are IP There is an IP-Input pair in for each time point, so the pair attribute is Time.  The Control attribute is the Pair attribute is the Time attribute.  The Control attribute is the attribute that differentiates between the IP and the Input group Input and IP groups, and in this example, it is the the ChIP attribute attribute.  Finally, the control the Control term is  is labeled as Input in the example. 

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.

• Absolute summit: base pair location of peak summit
• Pileup: pileup height at peak summit
• -log10(pvalue): negative log10 pvalue for the peak summit
• Fold enricment: fold enrichhment for thhe peak summit against random Poisson distribution with local lambda
• -log10(qvalue): negative log10 qvalue at peak summit
• a peak name generated by the MACS2 algorithm

Click the browse to peak button () to invoke chromosome view and zoom into that location.

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