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DNase I hypersensitive sites identification
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README.md

#Popera

###DNase I hypersensitive sites identification

####Dependncies:

samtools http://samtools.sourceforge.net

pysam http://code.google.com/p/pysam/

scipy http://www.scipy.org

numpy http://www.numpy.org

Author: Tao Zhang @ UW-Madison

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

####Options:

  • --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? http://en.wikipedia.org/wiki/Operatic_pop

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