ChipseqExample

Steps.

If you are starting with a CEL file:

cd Epigenetics/WaveGenerator/Chipchip

Use a bpmap file to perform the translation from CEL to BEDlike format.

python ChipchipCelToBed.py /path/file.CEL /path/Sc03b_MR_v04.bpmap

Place all of the BEDlike files in one directory (eg /path/BEDlike), then run

python ChipchipApplyBaseline.py /path/BEDlike/ /path/your.baseline /path/output/

Convert Bedlike files to Wig files:

python ChipchipBedlikeTowig.py /path/file.normalized.BEDlike

And run the wave generator on the file:

python TheWaveGenerator.py -data_file ~/Data/Phoebe_shift/baselined/2012-03-24\ H2A.Z_IP.normalized.wig -output_path ~/Data/Phoebe_shift/waves/ ~/git/Epigenetics/Epigenetics/testdata/wigtest.input