# make SPP output folders for individual replicates:
mkdir SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1
mkdir SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2
mkdir SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1
mkdir SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2
mkdir SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep1
mkdir SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep2
mkdir SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1
mkdir SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2

# make SPP output folders for pooled runs:
mkdir SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Pooled
mkdir SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Pooled
mkdir SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Pooled
mkdir SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Pooled

# make SPP output folders for pooled pseudoreplicates:
mkdir SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep1
mkdir SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep2
mkdir SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep1
mkdir SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep2
mkdir SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoRep1
mkdir SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoRep2
mkdir SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-PooledPseudoRep1
mkdir SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-PooledPseudoRep2

# make SPP output folders for individual pseudoreplicates:
mkdir SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoRep1
mkdir SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoRep2
mkdir SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoRep1
mkdir SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoRep2
mkdir SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoRep1
mkdir SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoRep2
mkdir SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoRep1
mkdir SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoRep2
mkdir SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep1PseudoRep1
mkdir SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep1PseudoRep2
mkdir SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep2PseudoRep1
mkdir SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep2PseudoRep2
mkdir SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1PseudoRep1
mkdir SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1PseudoRep2
mkdir SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2PseudoRep1
mkdir SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2PseudoRep2

# merge replicate BAM files:
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools merge A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.bam A549-100nM-Dex-1h-CTCF-Rep1-HA.36mers.unique.bam A549-100nM-Dex-1h-CTCF-Rep2-HA.36mers.unique.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools merge A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.bam A549-100nM-Dex-1h-1PCR_Input-Rep1-HA.36mers.unique.bam A549-100nM-Dex-1h-1PCR_Input-Rep1_V0422111-HA.36mers.unique.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools merge A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.bam A549-EtOH-1h-CTCF-Rep1-HA.36mers.unique.bam A549-EtOH-1h-CTCF-Rep2-HA.36mers.unique.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools merge A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.bam A549-EtOH-1h-1PCR_Input-Rep1-HA.36mers.unique.bam A549-EtOH-1h-1PCR_Input-V0416101-HA.36mers.unique.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools merge G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.bam G1E-CTCF-Rep1-PSU.36mers.unique.bam G1E-CTCF-Rep2-PSU.36mers.unique.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools merge G1E-CTCF-Rep1-vs-Rep2-PSU.Control.pooled.bam /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.bam /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools merge G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.ChIP.pooled.bam G1E-ER4-CTCF-Rep1-PSU.36mers.unique.bam G1E-ER4-CTCF-Rep2-PSU.36mers.unique.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools merge G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.Control.pooled.bam /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep1-ENCFF001MSM/G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.bam /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep2-ENCFF001MSW/G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.bam

# sort merged BAM files:
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools sort A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.bam A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools sort A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.bam A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools sort A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.bam A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools sort A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.bam A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools sort G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.bam G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.sorted
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools sort G1E-CTCF-Rep1-vs-Rep2-PSU.Control.pooled.bam G1E-CTCF-Rep1-vs-Rep2-PSU.Control.pooled.sorted
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools sort G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.ChIP.pooled.bam G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.ChIP.pooled.sorted
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools sort G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.Control.pooled.bam G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.Control.pooled.sorted

# index sorted BAM files:
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools index A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools index A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools index A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools index A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools index G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.sorted.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools index G1E-CTCF-Rep1-vs-Rep2-PSU.Control.pooled.sorted.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools index G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.ChIP.pooled.sorted.bam
/woldlab/castor/home/georgi/programs/samtools-0.1.18/samtools index G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.Control.pooled.sorted.bam

# Generate pseudoreplicates:
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py A549-100nM-Dex-1h-CTCF-Rep1-HA.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py A549-100nM-Dex-1h-CTCF-Rep2-HA.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py A549-100nM-Dex-1h-1PCR_Input-Rep1-HA.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py A549-100nM-Dex-1h-1PCR_Input-Rep1_V0422111-HA.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py A549-EtOH-1h-CTCF-Rep1-HA.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py A549-EtOH-1h-CTCF-Rep2-HA.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py A549-EtOH-1h-1PCR_Input-Rep1-HA.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py A549-EtOH-1h-1PCR_Input-V0416101-HA.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py G1E-CTCF-Rep1-vs-Rep2-PSU.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py G1E-CTCF-Rep1-PSU.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py G1E-CTCF-Rep2-PSU.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py G1E-ER4-CTCF-Rep1-PSU.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py G1E-ER4-CTCF-Rep2-PSU.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep1-ENCFF001MSM/G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep2-ENCFF001MSW/G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.bam

# Peak calls for individual replicates:
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-100nM-Dex-1h-CTCF-Rep1-HA.36mers.unique.bam -i=A549-100nM-Dex-1h-1PCR_Input-Rep1-HA.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-100nM-Dex-1h-CTCF-Rep2-HA.36mers.unique.bam -i=A549-100nM-Dex-1h-1PCR_Input-Rep1_V0422111-HA.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-EtOH-1h-CTCF-Rep1-HA.36mers.unique.bam -i=A549-EtOH-1h-1PCR_Input-Rep1-HA.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-EtOH-1h-CTCF-Rep2-HA.36mers.unique.bam -i=A549-EtOH-1h-1PCR_Input-V0416101-HA.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-CTCF-Rep1-PSU.36mers.unique.bam -i=/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-CTCF-Rep2-PSU.36mers.unique.bam -i=/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-ER4-CTCF-Rep1-PSU.36mers.unique.bam -i=/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep1-ENCFF001MSM/G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-ER4-CTCF-Rep2-PSU.36mers.unique.bam -i=/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep2-ENCFF001MSW/G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2

# Peak calls for for pooled datasets:
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.bam -i=A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Pooled
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.bam -i=A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Pooled
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.sorted.bam -i=G1E-CTCF-Rep1-vs-Rep2-PSU.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Pooled
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.ChIP.pooled.sorted.bam -i=G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Pooled

# Peak calls for for pooled pseudoreplicates:
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.pseudoRep1.bam -i=A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.pseudoRep2.bam -i=A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.pseudoRep1.bam -i=A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.pseudoRep2.bam -i=A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.sorted.pseudoRep1.bam -i=G1E-CTCF-Rep1-vs-Rep2-PSU.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.sorted.pseudoRep2.bam -i=G1E-CTCF-Rep1-vs-Rep2-PSU.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.ChIP.pooled.sorted.pseudoRep1.bam -i=G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.ChIP.pooled.sorted.pseudoRep2.bam -i=G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-PooledPseudoRep2

# Peak calls for for individual pseudoreplicates:
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-100nM-Dex-1h-CTCF-Rep1-HA.36mers.unique.pseudoRep1.bam -i=A549-100nM-Dex-1h-1PCR_Input-Rep1-HA.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-100nM-Dex-1h-CTCF-Rep1-HA.36mers.unique.pseudoRep2.bam -i=A549-100nM-Dex-1h-1PCR_Input-Rep1-HA.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-100nM-Dex-1h-CTCF-Rep2-HA.36mers.unique.pseudoRep1.bam -i=A549-100nM-Dex-1h-1PCR_Input-Rep1_V0422111-HA.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-100nM-Dex-1h-CTCF-Rep2-HA.36mers.unique.pseudoRep2.bam -i=A549-100nM-Dex-1h-1PCR_Input-Rep1_V0422111-HA.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-EtOH-1h-CTCF-Rep1-HA.36mers.unique.pseudoRep1.bam -i=A549-EtOH-1h-1PCR_Input-Rep1-HA.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-EtOH-1h-CTCF-Rep1-HA.36mers.unique.pseudoRep2.bam -i=A549-EtOH-1h-1PCR_Input-Rep1-HA.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-EtOH-1h-CTCF-Rep2-HA.36mers.unique.pseudoRep1.bam -i=A549-EtOH-1h-1PCR_Input-V0416101-HA.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=A549-EtOH-1h-CTCF-Rep2-HA.36mers.unique.pseudoRep2.bam -i=A549-EtOH-1h-1PCR_Input-V0416101-HA.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-CTCF-Rep1-PSU.36mers.unique.pseudoRep1.bam -i=/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-CTCF-Rep1-PSU.36mers.unique.pseudoRep2.bam -i=/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-CTCF-Rep2-PSU.36mers.unique.pseudoRep1.bam -i=/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-CTCF-Rep2-PSU.36mers.unique.pseudoRep2.bam -i=/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep2PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-ER4-CTCF-Rep1-PSU.36mers.unique.pseudoRep1.bam -i=/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep1-ENCFF001MSM/G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-ER4-CTCF-Rep1-PSU.36mers.unique.pseudoRep2.bam -i=/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep1-ENCFF001MSM/G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-ER4-CTCF-Rep2-PSU.36mers.unique.pseudoRep1.bam -i=/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep2-ENCFF001MSW/G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=G1E-ER4-CTCF-Rep2-PSU.36mers.unique.pseudoRep2.bam -i=/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep2-ENCFF001MSW/G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2PseudoRep2

# Clean up pseudoreplicate BAM files:
rm *.pooled.bam
rm *.sorted.bam
rm *.pseudoRep1.bam
rm *.pseudoRep2.bam
rm *.sorted.bamb.bai
rm *.pseudoRep1.bam.bai
rm *.pseudoRep2.bam.bai

# unzip peak call files:
gunzip SPP-300K*/*gz

# IDR for individual replicates:
Rscript batch-consistency-analysis.r SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1/A549-100nM-Dex-1h-CTCF-Rep1-HA.36mers.unique_VS_A549-100nM-Dex-1h-1PCR_Input-Rep1-HA.36mers.unique.regionPeak SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2/A549-100nM-Dex-1h-CTCF-Rep2-HA.36mers.unique_VS_A549-100nM-Dex-1h-1PCR_Input-Rep1_V0422111-HA.36mers.unique.regionPeak -1 IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1/A549-EtOH-1h-CTCF-Rep1-HA.36mers.unique_VS_A549-EtOH-1h-1PCR_Input-Rep1-HA.36mers.unique.regionPeak SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2/A549-EtOH-1h-CTCF-Rep2-HA.36mers.unique_VS_A549-EtOH-1h-1PCR_Input-V0416101-HA.36mers.unique.regionPeak -1 IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep1/G1E-CTCF-Rep1-PSU.36mers.unique_VS_G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.regionPeak SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep2/G1E-CTCF-Rep2-PSU.36mers.unique_VS_G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.regionPeak -1 IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1/G1E-ER4-CTCF-Rep1-PSU.36mers.unique_VS_G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.regionPeak SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2/G1E-ER4-CTCF-Rep2-PSU.36mers.unique_VS_G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.regionPeak -1 IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU 0 F signal.value

# IDR for pooled pseudoreplicates:
Rscript batch-consistency-analysis.r SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep1/A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.pseudoRep1_VS_A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep2/A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.pseudoRep2_VS_A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep1/A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.pseudoRep1_VS_A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoRep2/A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.ChIP.pooled.sorted.pseudoRep2_VS_A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoRep1/G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.sorted.pseudoRep1_VS_G1E-CTCF-Rep1-vs-Rep2-PSU.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoRep2/G1E-CTCF-Rep1-vs-Rep2-PSU.ChIP.pooled.sorted.pseudoRep2_VS_G1E-CTCF-Rep1-vs-Rep2-PSU.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-PooledPseudoRep1/G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.ChIP.pooled.sorted.pseudoRep1_VS_G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-PooledPseudoRep2/G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.ChIP.pooled.sorted.pseudoRep2_VS_G1E-ER4-CTCF-Rep1--vs-Rep2-PSU.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-PooledPseudoReps 0 F signal.value

# IDR for individual pseudoreplicates:
Rscript batch-consistency-analysis.r SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoRep1/A549-100nM-Dex-1h-CTCF-Rep1-HA.36mers.unique.pseudoRep1_VS_A549-100nM-Dex-1h-1PCR_Input-Rep1-HA.36mers.unique.pseudoRep1.regionPeak SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoRep2/A549-100nM-Dex-1h-CTCF-Rep1-HA.36mers.unique.pseudoRep2_VS_A549-100nM-Dex-1h-1PCR_Input-Rep1-HA.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoRep1/A549-100nM-Dex-1h-CTCF-Rep2-HA.36mers.unique.pseudoRep1_VS_A549-100nM-Dex-1h-1PCR_Input-Rep1_V0422111-HA.36mers.unique.pseudoRep1.regionPeak SPP-300K-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoRep2/A549-100nM-Dex-1h-CTCF-Rep2-HA.36mers.unique.pseudoRep2_VS_A549-100nM-Dex-1h-1PCR_Input-Rep1_V0422111-HA.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoRep1/A549-EtOH-1h-CTCF-Rep1-HA.36mers.unique.pseudoRep1_VS_A549-EtOH-1h-1PCR_Input-Rep1-HA.36mers.unique.pseudoRep1.regionPeak SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoRep2/A549-EtOH-1h-CTCF-Rep1-HA.36mers.unique.pseudoRep2_VS_A549-EtOH-1h-1PCR_Input-Rep1-HA.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoRep1/A549-EtOH-1h-CTCF-Rep2-HA.36mers.unique.pseudoRep1_VS_A549-EtOH-1h-1PCR_Input-V0416101-HA.36mers.unique.pseudoRep1.regionPeak SPP-300K-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoRep2/A549-EtOH-1h-CTCF-Rep2-HA.36mers.unique.pseudoRep2_VS_A549-EtOH-1h-1PCR_Input-V0416101-HA.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep1PseudoRep1/G1E-CTCF-Rep1-PSU.36mers.unique.pseudoRep1_VS_/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep1PseudoRep2/G1E-CTCF-Rep1-PSU.36mers.unique.pseudoRep2_VS_/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep2PseudoRep1/G1E-CTCF-Rep2-PSU.36mers.unique.pseudoRep1_VS_/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep2PseudoRep2/G1E-CTCF-Rep2-PSU.36mers.unique.pseudoRep2_VS_/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-Control-Rep1-ENCFF001MRP/G1E-ER4-Control-Rep1-ENCFF001MRP.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1PseudoRep1/G1E-ER4-CTCF-Rep1-PSU.36mers.unique.pseudoRep1_VS_/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep1-ENCFF001MSM/G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1PseudoRep2/G1E-ER4-CTCF-Rep1-PSU.36mers.unique.pseudoRep2_VS_/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep1-ENCFF001MSM/G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2PseudoRep1/G1E-ER4-CTCF-Rep2-PSU.36mers.unique.pseudoRep1_VS_/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep2-ENCFF001MSW/G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2PseudoRep2/G1E-ER4-CTCF-Rep2-PSU.36mers.unique.pseudoRep2_VS_/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-G1E/G1E-ER4-24h-Control-Rep2-ENCFF001MSW/G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2PseudoReps 0 F signal.value

# IDR plots for individual replicates:
Rscript batch-consistency-plot.r 1 IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA
Rscript batch-consistency-plot.r 1 IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU

# IDR plots for pooled pseudoreplicates:
Rscript batch-consistency-plot.r 1 IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoReps IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoReps IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoReps IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-PooledPseudoReps IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-PooledPseudoReps

# IDR plots individual pseudoreplicates:
Rscript batch-consistency-plot.r 1 IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoReps IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoReps IDR-SPP-A549-100nM-Dex-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoReps IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoReps IDR-SPP-A549-EtOH-1h-CTCF-Rep1-vs-Rep2-HA-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep1PseudoReps IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep2PseudoReps IDR-SPP-G1E-CTCF-Rep1-vs-Rep2-PSU-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1PseudoReps IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2PseudoReps IDR-SPP-G1E-ER4-CTCF-Rep1--vs-Rep2-PSU-Rep2PseudoReps

# compress peak call files:
gzip SPP-300K*/*eak