Filter peaks

After peak detection, you can filter peaks or annotated peaks to generate peaks of interest for downstream analysis.

Filter peaks based on peak table column criteria

The input for this task is a peaks-type data node.

• Choose a Peaks data node

• Click Filter peaks task in Peak analysis section in the pop-up menu (Figure 1)

The first drop-down menu allows you to choose to include or exclude base on the specified criteria.

The second drop-down menu allows you to choose any categorical or numeric information of the peaks to use for the filter criteria.

When you choose Sample name, or Chromosome, which are categorical information, the third drop-down menu will have is and is not as options. The fourth drop-down menu allows you to choose from the subgroups of the information (Figure 2).

When you select other information in the 2nd drop-down list, like Start, End, Length, Absolute summit, Pileup, -log10(pvalue), Fold enrichment or -log10(qvalue), which is numeric, the third drop-down includes:

• <: less than

• <=: less than or equal to

• ==: equal to

• >: greater than

• >=: greater than or equal to

The threshold is set using the text box (Figure 3). The input must be a number.\

When use OR and AND operators, you can build more advanced filter criteria:

When combining multiple filters all set to Include:

With AND, if all statements must be true for the sample to meet the filter criteria.

With OR, if any statement is true, the sample will meet the filter criteria.

When combining multiple filters all set to Exclude:

With AND, if any statement is true, the sample will meet the filter criteria.

With OR, all statements must be true for the sample to meet the filter criteria.

Filter annotated peaks based on a feature list

When you invoke filter peak task on a transcript/gene annotated peak data node, there is an additional option to filter peak regions based on a list of transcripts or genes (Figure 4).

Please see the Feature list filter chapter here.