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DNase I hypersensitive sites identification
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Poperalib change wiggle output Mar 26, 2015 change wiggle output Apr 6, 2015 add wig output Sep 27, 2014 Update May 30, 2014
requirements.txt add requirement May 22, 2014 Newadd May 20, 2014


###DNase I hypersensitive sites identification






Author: Tao Zhang @ UW-Madison

#####Example: python ~/Popera/ -d DH_sample1.bam,DH_sample2.bam -n sample1,sample2


  • --version show program's version number and exit

  • -h, --help show this help message and exit.

  • -d DATAFILES, --data=DATAFILES data file, should be sorted bam format, example=DH_sample1.bam,DH_sample2.bam

  • -n SAMPLENAMES, --name=SAMPLENAMES NH sample name default=DH_sample1,DH_sample2

  • -b BW, --bandwidth=BW kernel smooth band width, should >1, default=200

  • -t THRESHOLD, --threshold=THRESHOLD Hot spots threshold, default=4.0

  • -l MINLENGTH, --minlength=MINLENGTH minimum length of hot spots, default=5

  • --threads=NTHREADS threads number or cpu number, default=4

  • -w, --wig whether out put wiggle file, default=False

  • -x EXCLUDECHR, --excludechr=EXCLUDECHR Don't count those DHs, example='-x ChrM,ChrC'

What is Popera?

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