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        "author": "Nathan Ungerleider",
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        "description": "# SpliceV #\nVisualize coverage, canonical, and backsplice junctions.\n\n![Example plot](https://github.com/flemingtonlab/SpliceV/blob/master/etc/example.png)\n\n## Documentation ##\nSee https://splicev.readthedocs.io/en/master/\n\n## Example pipeline ##\nSee https://github.com/flemingtonlab/SpliceV/blob/master/docs/example.pdf\n\nThis will generate figure 1B and 1C from our manuscript (DOI pending)\n\n## Requirements ##\nSpliceV works with Python 2.7 and 3.0+.\n## Dependencies ##\n* Matplotlib\n* Numpy\n* pysam\n## Installation ##\nTo install SpliceV:\n\n```\npip install SpliceV\n```\n\nOr:\n\n```\ngit clone https://github.com/flemingtonlab/SpliceV.git\n```\n\n## Example ##\nTo run the example dataset:\n\n```\ngit clone https://github.com/flemingtonlab/SpliceV.git \n\ncd SpliceV/example \n\npython ../bin/SpliceV -b example.vta1.bam -gtf vta1.gtf -sj example.canonical.bed -bsj example.circles.bed -g VTA1 -f 3 -is 3\n\n```\n\nThe sample data comes from Akata cells (a B Cell Lymphoma line) that were treated with the exonuclease RNase R prior to sequencing. RNase R exclusively digests RNA with a free end, helping enrich circularized RNA abundance in the sample. \n\nThese example commands will generate the following plot:\n![User example plot](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1.png)\n\nThis plot reveals a prominant circle from exon 2 through exon 4 (evidenced by the back-splice junction reads which are plotted as curves below the axis. This is also demonstrated by the higher level of coverage in exon 2-4, shown by the relative intensity of color).\n\n![User example plot explained](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1_explained.png)\n\nThe major circularized isoform (exons 2-4; another less prevalent circle appears to include exon 5) is isolated below:\n\n\n![User example circle](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1_circ.png)\n\n## Authors ##\nCreated by Nathan Ungerleider and Erik Flemington\n\n\n",
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