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Tag pileup frequency (version 1.0.2)
Selecting combined requires paired-end BAM input
Requires paired-end BAM input

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.


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.