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#Popera

###DNase I hypersensitive sites identification

####Dependencies:

samtools http://samtools.sourceforge.net

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

scipy http://www.scipy.org

numpy http://www.numpy.org

pyBigWig https://github.com/deeptools/pyBigWig

Author: Tao Zhang @ UW-Madison & YZU

#####Example:

$ python Popera.py -d DNase.bam -n DNase --bigwig --threads 8

####Options:

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

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

  • -d DATAFILE, --data=DATAFILE data file, should be sorted bam format

  • -n SAMPLENAME, --name=SAMPLENAME NH sample name default=NH_sample

  • -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

  • --bigwig whether out put bigwig 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

Reference

Zhang T, Marand A, Jiang JM*: PlantDHS: A Database for DNase I Hypertensive Sites in Plants. Nucleic Acids Research 2016, 44(D1): D1148-D1153.

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