cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.bam -i=A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep1
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.bam -i=A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep2
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.bam -i=A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep1
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.bam -i=A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep2
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.ChIP.pooled.sorted.bam -i=IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.Control.pooled.sorted.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Pooled
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.ChIP.pooled.sorted.bam -i=IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.Control.pooled.sorted.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Pooled
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.ChIP.pooled.sorted.pseudoRep1.bam -i=IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.Control.pooled.sorted.pseudoRep1.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-PooledPseudoRep1
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.ChIP.pooled.sorted.pseudoRep2.bam -i=IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219.Control.pooled.sorted.pseudoRep2.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-PooledPseudoRep2
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.ChIP.pooled.sorted.pseudoRep1.bam -i=IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.Control.pooled.sorted.pseudoRep1.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-PooledPseudoRep1
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.ChIP.pooled.sorted.pseudoRep2.bam -i=IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221.Control.pooled.sorted.pseudoRep2.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-PooledPseudoRep2
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.pseudoRep1.bam -i=A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.pseudoRep1.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep1PseudoRep1
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.pseudoRep2.bam -i=A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.pseudoRep2.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep1PseudoRep2
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.pseudoRep1.bam -i=A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.pseudoRep1.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep2PseudoRep1
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.pseudoRep2.bam -i=A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.pseudoRep2.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-Dex-GR-Rep1-GSM2095218-vs-GSM2095219-Rep2PseudoRep2
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.pseudoRep1.bam -i=A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.pseudoRep1.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep1PseudoRep1
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=A549-EtOH-GR-Rep1-GSM2095220.hg20-male.36mers.unique.pseudoRep2.bam -i=A549-Dex-GR-Rep1-GSM2095218.hg20-male.36mers.unique.pseudoRep2.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep1PseudoRep2
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.pseudoRep1.bam -i=A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.pseudoRep1.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep2PseudoRep1
cd /N/dc2/projects/marinovg/papers/2017-ENCODE-enhancers/2016-09-15-mm10-hg20-migration-A549; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=A549-EtOH-GR-Rep2-GSM2095221.hg20-male.36mers.unique.pseudoRep2.bam -i=A549-Dex-GR-Rep2-GSM2095219.hg20-male.36mers.unique.pseudoRep2.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-IDR-A549-EtOH-GR-Rep1-GSM2095220-vs-GSM2095221-Rep2PseudoRep2