In this section, we will create a list of peaks significantly enriched in the ChIP sample versus the control sample.
Select Create a list of enriched regions from the Peak Analysis section of the ChIP-Seq workflow
Select Specify New Criteria (Figure 1)
Figure 1. List creator for ChIP-Seq data allows you to create lists using preset or custom criteria
Configure the new criteria as shown (Figure 2).
Name the criteria p-value filtered
Select 1/regions (peaks) from the Spreadsheet drop-down menu
Select 11. p-value(Sample ID vs. mock) from the Column drop-down menu
Select significant with FDR of from the include p-values drop-down menu with a value of 0.05
Figure 2. Creating a criteria that includes regions significantly enriched in ChIP vs. mock
Select OK to add the criteria to the criteria list (Figure 3)
Figure 3. New criteria are added to the criteria list
Select Save
Select p-value filtered from the list of criteria (Figure 4)
Figure 4. Choosing criteria to save as lists
Select OK
The new spreadsheet will open (Figure 5).
Figure 5. Spreadsheet with regions that are significantly enriched in the ChIP sample vs. control
Other List Creator operations like the Venn Diagram, Union (Or), and Intersection (And) of the lists could be used to create different lists of enriched peaks. For example, you could filter on the intersection between Strand Separation FDR of 0.05 and Peaks not in mock or filter by scaled fold change or apply a minimum number of reads per million. The choice of what peaks you want to consider for downstream analysis depends on the goals and details of your experimental design.
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