What it does

Generates a frequency pileup of the 5' ends of aligned reads in a BAM file relative to reference points in a BED file.

Options

Global transformations

• 5' to 3' tag shift (bp) - moves all tags from the 5' to the 3' direction given a specified distance in base pairs.
• Bin Size (bp) - bins tags together into specified size, useful for lower resolution data or for especially wide reference windows.
• Set Tags to be equal - standardizes tag count to be equal to genome size, useful for replicate comparisons.

Read parameters

• Reads to Examine - output data for Read1, Read2, or combined (only for paired end BAM files).
• Require Proper PE - require output reads to be properly paired (only for paired end BAM files).
• Combine Strands - examine reads on a forward/reverse basis (strand separate) or ignoring read orientation (strand combined).

Run parameters

• Composite smoothing window (bp) - sliding window to smooth composite frequencies.
• Output frequencies for heatmap - generate an additional dataset collection containing frequencies that can be used to generate a heatmap plot.