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