View Source

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)

Genomics Suite Documentation > Creating a list of enriched regions > 2017-07-26 12_30_42-List Creator.png

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

Genomics Suite Documentation > Creating a list of enriched regions > 2017-07-26 12_31_13-Configure Criteria.png

Select OK to add the criteria to the criteria list (Figure 3)

Genomics Suite Documentation > Creating a list of enriched regions > 2017-07-26 12_31_31-List Creator.png

Select Save
Select p-value filtered from the list of criteria (Figure 4)

Genomics Suite Documentation > Creating a list of enriched regions > 2017-07-26 12_31_39-List Creator.png

Select OK

The new spreadsheet will open (Figure 5).

Genomics Suite Documentation > Creating a list of enriched regions > 2017-08-09 14_16_22-Partek Genomics Suite - 1_p-value_filtered (p-value filtered.txt).png

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.