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.