tools.shiftBigwigs

Help Info

Slide bigwigs to turn mnase endpoint data into midpoints.

usage: shiftBigwigs [-h] [--bw5 BW5] [--bw3 BW3] [--scan]
                    [--mnase] [--out OUT]

Named Arguments

--bw5

The first (5’) bigwig file.

--bw3

The second (3’) bigwig file.

--scan

Measure the cross-correlation between the bigwigs and display a plot.

Default: False

--mnase

Perform the +79, -80 shift that is recommended for mnase

Default: False

--out

The name of the bigwig file to write, or, if scanning, the name of the dat file containing the correlation.

Usage

A little script to shift and combine bigwig tracks.

bpreveal.tools.shiftBigwigs.scanBigwigs(bwFname1, bwFname2, outFname)

Show a plot of the correlation between the two bigwigs, and save data to outFname.

Parameters:

  • bwFname1 (str)

  • bwFname2 (str)

  • outFname (str)

bpreveal.tools.shiftBigwigs.doShift(bwFnames, shifts, outFname)

Actually shift the files.

Parameters:

  • bwFnames (list[str])

  • shifts (list[int])

  • outFname (str)

bpreveal.tools.shiftBigwigs.getParser()

Generate (but don’t call parse_args()) the parser.

bpreveal.tools.shiftBigwigs.main()

Run the program.