bedGraph helpers

bedGraph helpers are used for converting interval-style signal tracks to nucleotide-level tables and for smoothing RPM density tracks.

Input bedGraph format

Both commands expect a tab-delimited bedGraph-like file without a header:

chrom    start    end    value

Coordinates follow the standard 0-based, half-open interval style used by bedGraph:

chr1    100    103    2.5

represents positions 100-101, 101-102, and 102-103 with value 2.5.

rpm_smooth

Function

Smooth RPM density in bedGraph files. The command first expands interval bins to single-nucleotide bins, fills missing positions with zero, smooths values chromosome by chromosome, clips negative smoothed values to zero, and writes a bedGraph-like output.

Parameters

Parameter	Meaning
-i	Input bedGraph file.
-o	Output smoothed bedGraph file.
-m	Smoothing method: SG for Savitzky-Golay or Gaus for Gaussian. Default: SG.
-w	Window width for Savitzky-Golay smoothing. Default: 11.
-p	Polynomial order for Savitzky-Golay smoothing. Default: 3.
-s	Gaussian sigma. Default: 1.
-z	Remove rows with smoothed RPM equal to zero. Default: keep zero rows.

Savitzky-Golay example

rpm_smooth \
  -i sample.rpm.bedgraph \
  -m SG \
  -w 11 \
  -p 3 \
  -z \
  -o sample.rpm.SG.bedgraph

Gaussian example

rpm_smooth \
  -i sample.rpm.bedgraph \
  -m Gaus \
  -s 2 \
  -z \
  -o sample.rpm.Gaus.bedgraph

Notes

• rpm_smooth can generate dense chromosome-wide single-nucleotide output. For large genomes, run it per chromosome or on filtered regions when possible.
• For Savitzky-Golay smoothing, the window width should be appropriate for the expected signal shape. Very small windows may under-smooth, while very large windows may flatten true peaks.
• Use -z when you want a compact bedGraph output without zero-coverage positions.