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 can be used with or without control sample.
MACS2 dialog
Selecting MACS2 from the context sensitive menu will bring up the MACS2 task dialog, interface will be different depends whether there are sample attributes available in the data tab. If there are only two sample for instance, ChIP and mock as sample name, there is no attribute assigned to the two samples, the dialog will look like (Figure 1).
Figure 1. MACS2 dialog: manually add ChIP vs control pairs for peak detection
If the selected aligned data node was imported, reference assembly the data aligned to needs to be specified, choose the assembly the sequence aligned to from the drop-down list; if the alignment was performed in Partek Flow, this option will not appear.
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 panel on the top-right, choose control sample to put 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 added, the samples will be combined (or pooled) in the analysis.
If the sample attributes are defined, you will have an additional option to add pairs based on the attribute. For instance Figure 2 is show an example data with 4 samples, 2 time point, there in one ChIP sample and one input sample in each time point.
Figure 2. Experiment example data illustrate sample with two attributes: IP and Time
When select MACS2 task, the default option is to use sample attribute to add multiple pairs at one button click (Figure 3)
Figure 3. Specify IP vs control pairs based on sample attributes
There are IP-Input pair in each time point, so the pair attribute is Time; Control attribute is the attribute contains IP and input group, which is ChIP, the control term is labeled as Input in the example, when click Generate pairs, the two pairs will be automatically added to the Pairs table at once (Figure 4).
Figure 4. Two IP vs input sample pairs are added in the Pairs table
References
- Zhang Y, Liu T, et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
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