mkdir /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-08-31-Figs
cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-08-31-Figs
===============================================================================
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.bz2 | wc -l
32279 peaks
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.bz2 | head -501 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.top500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.bz2 | head -501 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.top500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.bz2 | head -501 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.top500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.bz2 | head -501 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.top500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.bz2 | head -501 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.top500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.bz2 | head -1 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.bottom500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.bz2 | head -1 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.bottom500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.bz2 | head -1 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.bottom500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.bz2 | head -1 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.bottom500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.bz2 | head -1 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.bottom500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.bz2 | tail -500 >> signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.bottom500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.bz2 | tail -500 >> signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.bottom500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.bz2 | tail -500 >> signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.bottom500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.bz2 | tail -500 >> signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.bottom500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.bz2 | tail -500 >> signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.bottom500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.bz2 | head -1 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.middle500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.bz2 | head -1 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.middle500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.bz2 | head -1 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.middle500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.bz2 | head -1 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.middle500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.bz2 | head -1 > signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.middle500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.bz2 | head -16139 | tail -500 >> signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.middle500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.bz2 | head -16139 | tail -500 >> signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.middle500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.bz2 | head -16139 | tail -500 >> signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.middle500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.bz2 | head -16139 | tail -500 >> signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.middle500 &
bzip2 -cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-06-09-C2C12-heatmaps/signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.bz2 | head -16139 | tail -500 >> signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.middle500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.bottom500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.middle500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.top500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.bottom500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.middle500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.top500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.bottom500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.middle500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.top500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.bottom500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.middle500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.top500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.bottom500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.middle500 &
bzip2 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.top500 &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.bottom500.bz2 1 0.4 0 .5 Reds 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.bottom500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.middle500.bz2 1 0.4 0 .5 Reds 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.middle500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.top500.bz2 1 0.4 0 .5 Reds 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-myogenin-16273-vs-16495.top500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.bottom500.bz2 1 0.4 0 .5 Reds 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.bottom500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.middle500.bz2 1 0.4 0 .5 Reds 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.middle500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.top500.bz2 1 0.4 0 .5 Reds 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-60h-p300-37C-16274-vs-16507.top500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.bottom500.bz2 1 0.4 0 .5 Reds 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.bottom500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.middle500.bz2 1 0.4 0 .5 Reds 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.middle500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.top500.bz2 1 0.4 0 .5 Reds 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-DNAse.top500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.bottom500.bz2 1 0.4 0 .5 Reds 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.bottom500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.middle500.bz2 1 0.4 0 .5 Reds 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.middle500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.top500.bz2 1 0.4 0 .5 Reds 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.C2C12-myocyte-H3K27ac.top500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.bottom500.bz2 1 0.4 0 .1 binary 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.bottom500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.middle500.bz2 1 0.4 0 .1 binary 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.middle500.png &
python /woldlab/castor/home/georgi/code/plotting/heatmap.py signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.top500.bz2 1 0.4 0 .1 binary 5,400 signal-around-SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.RRCAGSTG.top500.png &
python /woldlab/castor/home/georgi/code/ChIP/regionIntersection_BigDataSets-overlapping_regions.py /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-HepG2/HepG2-DNAse.pooled.sorted.MACS-2.1.0.p1e-1_peaks.IDR_0.05.narrowPeak 0 /woldlab/castor/home/georgi/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.TSS-1kb_radius.bed 0 HepG2-DNAse-vs-TSS &
python /woldlab/castor/home/georgi/code/ChIP/regionIntersection_BigDataSets-overlapping_regions.py /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-K562/K562-DNAse.pooled.sorted.MACS-2.1.0.p1e-1_peaks.IDR_0.05.narrowPeak 0 /woldlab/castor/home/georgi/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.TSS-1kb_radius.bed 0 K562-DNAse-vs-TSS &
rm K562-DNAse-vs-TSS-intersection2
rm K562-DNAse-vs-TSS-outersection2
rm HepG2-DNAse-vs-TSS-intersection2
rm HepG2-DNAse-vs-TSS-outersection2
python /woldlab/castor/home/georgi/code/ChIP/regionIntersection_BigDataSets-overlapping_regions.py HepG2-DNAse-vs-TSS-intersection1 0 K562-DNAse-vs-TSS-intersection1 0 HepG2-vs-K562-TSS-proximal &
python /woldlab/castor/home/georgi/code/ChIP/regionIntersection_BigDataSets-overlapping_regions.py HepG2-DNAse-vs-TSS-outersection1 0 K562-DNAse-vs-TSS-outersection1 0 HepG2-vs-K562-TSS-distal &
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/C2C12_cREs.txt 36 Figure3data/C2C12_cREs.myogenin-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/C2C12_cREs.txt 39 Figure3data/C2C12_cREs.p300-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/C2C12_cREs.txt 41 Figure3data/C2C12_cREs.DNAse-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/C2C12_cREs.txt 43 Figure3data/C2C12_cREs.H3K27ac-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/Gata1_Cons_cREs.txt 12 Figure3data/Gata1_Cons_cREs.DNAse-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/Gata1_Cons_cREs.txt 13 Figure3data/Gata1_Cons_cREs.H3K27ac-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/Gata1_Cons_cREs.txt 10 Figure3data/Gata1_Cons_cREs.GATA1-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/Gata1_Cons_cREs.txt 16 Figure3data/Gata1_Cons_cREs.TAL1-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/Gata1_cREs.txt 14 Figure3data/Gata1_cREs.DNAse-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/Gata1_cREs.txt 15 Figure3data/Gata1_cREs.H3K27ac-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/Gata1_cREs.txt 12 Figure3data/Gata1_cREs.GATA1-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/Gata1_cREs.txt 18 Figure3data/Gata1_cREs.TAL1-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/HepG2_SOM_cREs.txt 27 Figure3data/HepG2_SOM_cREs.H3K27ac-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/HepG2_SOM_cREs.txt 18 Figure3data/HepG2_SOM_cREs.DNAse-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/K562_chromHMM_cREs.txt 46 Figure3data/K562_chromHMM_cREs.H3K27ac-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/K562_chromHMM_cREs.txt 45 Figure3data/K562_chromHMM_cREs.DNAse-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/K562_TF_cREs.txt 95 Figure3data/K562_TF_cREs.DNAse-cdf
python /woldlab/castor/home/georgi/code/empiricalCDF.py Figure3data/K562_TF_cREs.txt 95 Figure3data/K562_TF_cREs.H3K27ac-cdf
ls -1 ../*/*myogen*RPM*
python /woldlab/castor/home/georgi/code/ChIP/regionIntersection_BigDataSets-overlapping_regions.py ../2017-07-20-myogenin-DHS-H3K27ac-RPM/C2C12-myocyte-IDR0.05-H3K27ac-vs-DHS-intersection1.C2C12-myocyte-myogenin-RT-5273-IP-E4-5261-16273.RPM.bz2 0 ../datasets-C2C12/SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.narrowPeak.RPM 0 C2C12-myocyte-IDR0.05-H3K27ac-vs-DHS-intersection1-vs-C2C12-60h-myogenin
python /woldlab/castor/home/georgi/code/empiricalCDF.py C2C12-myocyte-IDR0.05-H3K27ac-vs-DHS-intersection1-vs-C2C12-60h-myogenin-intersection1 10 C2C12-myocyte-IDR0.05-H3K27ac-vs-DHS-intersection1-vs-C2C12-60h-myogenin-intersection1-myogenin-cdf -step 50
python /woldlab/castor/home/georgi/code/ChIP/regionIntersection_BigDataSets-overlapping_regions.py ../2017-07-20-myogenin-DHS-H3K27ac-RPM/C2C12-myocyte-IDR0.05-H3K27ac-vs-DHS-intersection1.C2C12-myocyte-DNAse-Rep1.RPM.bz2 0 ../datasets-C2C12/SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.narrowPeak.RPM 0 C2C12-myocyte-IDR0.05-H3K27ac-vs-DHS-intersection1-vs-C2C12-60h-myogenin.DNAse &
python /woldlab/castor/home/georgi/code/ChIP/regionIntersection_BigDataSets-overlapping_regions.py ../2017-07-20-myogenin-DHS-H3K27ac-RPM/C2C12-myocyte-IDR0.05-H3K27ac-vs-DHS-intersection1.C2C12-myocyte-H3K27ac-AM_39113_31814008-RT_Fix_5158-5933_IP_B3-17875.RPM.bz2 0 ../datasets-C2C12/SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled.IDR_0.05.narrowPeak.RPM 0 C2C12-myocyte-IDR0.05-H3K27ac-vs-DHS-intersection1-vs-C2C12-60h-myogenin.H3K27ac &
python /woldlab/castor/home/georgi/code/empiricalCDF.py C2C12-myocyte-IDR0.05-H3K27ac-vs-DHS-intersection1-vs-C2C12-60h-myogenin.DNAse-intersection1 10 C2C12-myocyte-IDR0.05-H3K27ac-vs-DHS-intersection1-vs-C2C12-60h-myogenin.DNAse-intersection1-cdf -step 50
python /woldlab/castor/home/georgi/code/empiricalCDF.py C2C12-myocyte-IDR0.05-H3K27ac-vs-DHS-intersection1-vs-C2C12-60h-myogenin.H3K27ac-intersection1 10 C2C12-myocyte-IDR0.05-H3K27ac-vs-DHS-intersection1-vs-C2C12-60h-myogenin.H3K27ac-intersection1-cdf -step 50
ls -1 ../*/*G1E*RPM*
cat ../datasets-G1E/SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Pooled.IDR_0.05.narrowPeak ../datasets-G1E/SPP-300K-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-Pooled.IDR_0.05.narrowPeak ../datasets-G1E/SPP-300K-G1E-TAL1-ENCFF001MPN-vs-ENCFF001MPP-Pooled.IDR_0.05.narrowPeak > G1E-TF.IDR_0.05.narrowPeak
python /woldlab/castor/home/georgi/code/ChIP/regionIntersection_BigDataSets-overlapping_regions.py ../2016-10-23-erythroid-plots/G1E-ER4-IDR-0.05.DNAse-vs-H3K27ac-intersection1.DNAse_RPM.bz2 0 G1E-TF.IDR_0.05.narrowPeak 0 G1E-ER4-IDR-0.05.DNAse-vs-H3K27ac-intersection1.DNAse_RPM-vs-G1E-TF &
python /woldlab/castor/home/georgi/code/ChIP/regionIntersection_BigDataSets-overlapping_regions.py ../2016-10-23-erythroid-plots/G1E-ER4-IDR-0.05.DNAse-vs-H3K27ac-intersection1.H3K27ac_RPM.bz2 0 G1E-TF.IDR_0.05.narrowPeak 0 G1E-ER4-IDR-0.05.DNAse-vs-H3K27ac-intersection1.H3K27ac_RPM-vs-G1E-TF &
python /woldlab/castor/home/georgi/code/empiricalCDF.py G1E-ER4-IDR-0.05.DNAse-vs-H3K27ac-intersection1.DNAse_RPM-vs-G1E-TF-intersection1 11 G1E-ER4-IDR-0.05.DNAse-vs-H3K27ac-intersection1.DNAse_RPM-vs-G1E-TF-intersection1-cdf -step 50
python /woldlab/castor/home/georgi/code/empiricalCDF.py G1E-ER4-IDR-0.05.DNAse-vs-H3K27ac-intersection1.H3K27ac_RPM-vs-G1E-TF-intersection1 11 G1E-ER4-IDR-0.05.DNAse-vs-H3K27ac-intersection1.H3K27ac_RPM-vs-G1E-TF-intersection1-cdf -step 50
ls -1 ../*/*HepG2*RPM*
ls -1 ../*/*K562*RPM*
python /woldlab/castor/home/georgi/code/empiricalCDF.py ../2016-12-23-figures/HepG2-intersects/HepG2-DNAse-vs-H3K27ac-intersection1.DNAse.RPM.bz2 10 HepG2-DNAse-vs-H3K27ac-intersection1.DNAse.RPM-cdf -step 50
python /woldlab/castor/home/georgi/code/empiricalCDF.py ../2016-12-23-figures/HepG2-intersects/HepG2-DNAse-vs-H3K27ac-intersection1.H3K27ac.RPM.bz2 10 HepG2-DNAse-vs-H3K27ac-intersection1.H3K27ac.RPM-cdf -step 50
python /woldlab/castor/home/georgi/code/empiricalCDF.py ../2016-12-23-figures/K562-intersects/K562-DNAse-vs-H3K27ac-intersection1.DNAse.RPM.bz2 10 K562-DNAse-vs-H3K27ac-intersection1.DNAse.RPM-cdf -step 50
python /woldlab/castor/home/georgi/code/empiricalCDF.py ../2016-12-23-figures/K562-intersects/K562-DNAse-vs-H3K27ac-intersection1.H3K27ac.RPM.bz2 10 K562-DNAse-vs-H3K27ac-intersection1.H3K27ac.RPM-cdf -step 50
python /woldlab/castor/home/georgi/code/makehistogram.py /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/DESeq2-regions-200bp/IDR-0.05-A549-GR.200bp-radius.combined_end1_50K.SFR.readCounts.input-vs-Dex.fixed.p-adj-0.05-up.GR-only 2 /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/DESeq2-regions-200bp/IDR-0.05-A549-GR.200bp-radius.combined_end1_50K.SFR.readCounts.input-vs-Dex.fixed.p-adj-0.05-up.GR-only-lFC-hist -bins 0.2 -4.5 0
python /woldlab/castor/home/georgi/code/makehistogram.py /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/DESeq2-regions-200bp/IDR-0.05-A549-GR.200bp-radius.combined_end1_50K.SFR.readCounts.input-vs-ETOH.fixed.p-adj-0.05-up.GR-only 2 /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/DESeq2-regions-200bp/IDR-0.05-A549-GR.200bp-radius.combined_end1_50K.SFR.readCounts.input-vs-ETOH.fixed.p-adj-0.05-up.GR-only-lFC-hist -bins 0.2 -4.5 0
=====================================================================================================
cd /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/
python /woldlab/castor/home/georgi/code/bedRPKMfromBAM.py /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/DESeq2-regions-200bp/IDR-0.05-A549-GR.200bp-radius.combined_end1_50K.SFR.readCounts.input-vs-Dex.fixed.txt.GR-only.baseMean5.bed 0 /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-A549/A549-EtOH-GR-Rep1-GSM2095220-seems-to-be-Dex/A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.bam /woldlab/castor/home/georgi/genomes/hg20/hg38.chrom.sizes /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/DESeq2-regions-200bp/IDR-0.05-A549-GR.200bp-radius.combined_end1_50K.SFR.readCounts.input-vs-Dex.fixed.txt.GR-only.baseMean5.A549-Dex-GR.RPM -RPM -uniqueBAM &
python /woldlab/castor/home/georgi/code/bedRPKMfromBAM.py /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/DESeq2-regions-200bp/IDR-0.05-A549-GR.200bp-radius.combined_end1_50K.SFR.readCounts.input-vs-ETOH.fixed.txt.GR-only.baseMean6.6.bed 0 /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-A549/A549-EtOH-GR-Rep1-GSM2095220-seems-to-be-Dex/A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.bam /woldlab/castor/home/georgi/genomes/hg20/hg38.chrom.sizes /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/DESeq2-regions-200bp/IDR-0.05-A549-GR.200bp-radius.combined_end1_50K.SFR.readCounts.input-vs-ETOH.fixed.txt.GR-only.baseMean6.6.A549-Dex-GR.RPM -RPM -uniqueBAM &
python /woldlab/castor/home/georgi/code/combineIntoTable.py DESeq2-regions-200bp.ReadPass.ChIP-RPM.files DESeq2-regions-200bp.ReadPass.ChIP-RPM.table
python /woldlab/castor/home/georgi/code/combineIntoTable.py DESeq2-regions-200bp.active.files DESeq2-regions-200bp.active.table -union -NaN 0
python /woldlab/castor/home/georgi/code/combineIntoTable.py DESeq2-regions-200bp.active.ChIP-RPM.files DESeq2-regions-200bp.active.ChIP-RPM.table
python /woldlab/castor/home/georgi/code/MatrixToCDT.py DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.table 0 1:6 DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.mat-cdt -order /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/clustering/DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.lfc-only.cdt-order 0
python /woldlab/castor/home/georgi/code/MatrixToCDT.py DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.lfc-only.table 0 1:2 DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.lfc-only.mat-cdt -order /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/clustering/DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.cdt-order 0
python /woldlab/castor/home/georgi/code/extractDataFromAListOfGenes.py DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.table /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/clustering/DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.lfc-only.cdt.common 0 DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.table.common -header
python /woldlab/castor/home/georgi/code/extractDataFromAListOfGenes.py DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.table /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/clustering/DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.lfc-only.cdt.Dex-only 0 DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.table.Dex-only -header
python /woldlab/castor/home/georgi/code/extractDataFromAListOfGenes.py DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.table /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/2017-01-20-STARR-seq/clustering/DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.lfc-only.cdt.EtOH-only 0 DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.table.EtOH-only -header
python /woldlab/castor/home/georgi/code/multiple-fields-histogram.py DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.table.common 1-6 string DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.table.common-multi-hist
python /woldlab/castor/home/georgi/code/multiple-fields-histogram.py DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.table.Dex-only 1-6 string DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.table.Dex-only-multi-hist
python /woldlab/castor/home/georgi/code/multiple-fields-histogram.py DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.table.EtOH-only 1-6 string DESeq2-regions-200bp.active.ChIP-RPM.sfr.0h-3h.peak-calls-only.table.EtOH-only-multi-hist
python /woldlab/castor/home/georgi/code/MatrixToCDT.py combined.table.peak-calls-only-p300-DNAse-H3K27ac 0 1:6 combined.table.peak-calls-only-p300-DNAse-H3K27ac.mat-cdt -order combined.table.fc-only.cdt-order 0
python /woldlab/castor/home/georgi/code/MatrixToCDT.py combined.table.peak-calls-only 0 2:3 combined.table.peak-calls-only-MyoD-myogenin.mat-cdt -order combined.table.fc-only.cdt-order 0
python /woldlab/castor/home/georgi/code/multiple-fields-histogram.py MB_Functional.txt 25-40 string MB_Functional.txt-multi-hist
python /woldlab/castor/home/georgi/code/multiple-fields-histogram.py MB+MC_Functional.txt 25-40 string MB+MC_Functional.txt-multi-hist
python /woldlab/castor/home/georgi/code/multiple-fields-histogram.py MC_Functional.txt 25-40 string MC_Functional.txt-multi-hist
python /woldlab/castor/home/georgi/code/multiple-fields-histogram.py NotFunctional.txt 25-40 string NotFunctional.txt-multi-hist