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)
- Return type:
None
- bpreveal.tools.shiftBigwigs.doShift(bwFnames, shifts, outFname)
Actually shift the files.
- Parameters:
bwFnames (list[str])
shifts (list[int])
outFname (str)
- Return type:
None
- bpreveal.tools.shiftBigwigs.getParser()
Generate (but don’t call parse_args()) the parser.
- Return type:
ArgumentParser
- bpreveal.tools.shiftBigwigs.main()
Run the program.
- Return type:
None