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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 lianged ata aligned data node was generated by Partek Flow, this option will not appear.

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The 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 – human Homo sapiens, size is 2.7e9

mm – mouse Mus musculus, size is 1.87e9

ce – C. Caenorhabditis elegans, size is 9e7

dm – fruit fly Drosophila melongaster, size is 1.2e8

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

When sample attribute is not For data where no sample attributes were specified, for instance there are only two sample -- ChIP and mock as sample namesamples, the peak detection pairs needs to be manually defined (Figure 1). In the example in Figure 1, in the Define pairs section, the left panel list lists all the sample names , add (chip and mock) .  Add one pair at a time , select ChIP by selecting the chip sample to put in the IP panel on the top-right, choose control sample to put and selecting the mock sample 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 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 based on the attribute. For instance Figure 3 is show  shows an example data with 4 samples, 2 time pointpoints, and there in is one ChIP IP sample and one input Input sample in each time point.

When select running the MACS2 task, the default option is will be to use sample attribute to add multiple pairs at one button with a single mouse click (Figure 4). 

There are IP-Input pair in each time point, so the pair attribute is Time; .  The Control attribute is the attribute contains that differentiates between the IP and input the Input group, which is ChIPand in this example, it is the ChIP attribute.  Finally, the control term is labeled as Input in the example, when click .  Click Generate pairs,  and the two pairs will be automatically added to the Pairs table at once (Figure 5).

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In the task report, each pair will generate a list of peaks displayed in a table (Figure 6).

• Absolute summit: base pair location of peak summit
• Pileup: pileup height at peak summit
• -log10(pvalue): negative log10 pvalue for

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

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

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