# make SPP output folders for individual replicates:
mkdir SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep1
mkdir SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep2
mkdir SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1
mkdir SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep2

# make SPP output folders for pooled runs:
mkdir SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Pooled
mkdir SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Pooled

# make SPP output folders for pooled pseudoreplicates:
mkdir SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoRep1
mkdir SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoRep2
mkdir SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-PooledPseudoRep1
mkdir SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-PooledPseudoRep2

# make SPP output folders for individual pseudoreplicates:
mkdir SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep1PseudoRep1
mkdir SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep1PseudoRep2
mkdir SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep2PseudoRep1
mkdir SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep2PseudoRep2
mkdir SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1PseudoRep1
mkdir SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1PseudoRep2
mkdir SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep2PseudoRep1
mkdir SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep2PseudoRep2

# merge replicate BAM files:
samtools merge G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.bam G1E-GATA1-Rep1-ENCFF001MOE.mm10.36mers.unique.bam G1E-GATA1-Rep2-ENCFF001MOM.mm10.36mers.unique.bam
samtools merge G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.Control.pooled.bam G1E-Control-Rep1-ENCFF001MOR.mm10.36mers.unique.bam G1E-Control-Rep2-ENCFF001MPG.mm10.36mers.unique.30M.bam
samtools merge G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.ChIP.pooled.bam G1E-ER4-24h-GATA1-Control-Rep1-ENCFF001MRX.mm10.36mers.unique.bam G1E-ER4-24h-GATA1-Control-Rep2-ENCFF001MSL.mm10.36mers.unique.bam
samtools merge G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.Control.pooled.bam G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.bam G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.30M.bam

# sort merged BAM files:
samtools sort G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.bam G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.sorted
samtools sort G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.Control.pooled.bam G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.Control.pooled.sorted
samtools sort G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.ChIP.pooled.bam G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.ChIP.pooled.sorted
samtools sort G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.Control.pooled.bam G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.Control.pooled.sorted

# index sorted BAM files:
samtools index G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.sorted.bam
samtools index G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.Control.pooled.sorted.bam
samtools index G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.ChIP.pooled.sorted.bam
samtools index G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.Control.pooled.sorted.bam

# Generate pseudoreplicates:
python /N/dc2/projects/marinovg/code-new/BAMPseudoReps.py G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.sorted.bam
python /N/dc2/projects/marinovg/code-new/BAMPseudoReps.py G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.Control.pooled.sorted.bam
python /N/dc2/projects/marinovg/code-new/BAMPseudoReps.py G1E-GATA1-Rep1-ENCFF001MOE.mm10.36mers.unique.bam
python /N/dc2/projects/marinovg/code-new/BAMPseudoReps.py G1E-GATA1-Rep2-ENCFF001MOM.mm10.36mers.unique.bam
python /N/dc2/projects/marinovg/code-new/BAMPseudoReps.py G1E-Control-Rep1-ENCFF001MOR.mm10.36mers.unique.bam
python /N/dc2/projects/marinovg/code-new/BAMPseudoReps.py G1E-Control-Rep2-ENCFF001MPG.mm10.36mers.unique.30M.bam
python /N/dc2/projects/marinovg/code-new/BAMPseudoReps.py G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.ChIP.pooled.sorted.bam
python /N/dc2/projects/marinovg/code-new/BAMPseudoReps.py G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.Control.pooled.sorted.bam
python /N/dc2/projects/marinovg/code-new/BAMPseudoReps.py G1E-ER4-24h-GATA1-Control-Rep1-ENCFF001MRX.mm10.36mers.unique.bam
python /N/dc2/projects/marinovg/code-new/BAMPseudoReps.py G1E-ER4-24h-GATA1-Control-Rep2-ENCFF001MSL.mm10.36mers.unique.bam
python /N/dc2/projects/marinovg/code-new/BAMPseudoReps.py G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.bam
python /N/dc2/projects/marinovg/code-new/BAMPseudoReps.py G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.30M.bam

# Peak calls for individual replicates:
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-GATA1-Rep1-ENCFF001MOE.mm10.36mers.unique.bam -i=G1E-Control-Rep1-ENCFF001MOR.mm10.36mers.unique.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep1
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-GATA1-Rep2-ENCFF001MOM.mm10.36mers.unique.bam -i=G1E-Control-Rep2-ENCFF001MPG.mm10.36mers.unique.30M.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep2
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-ER4-24h-GATA1-Control-Rep1-ENCFF001MRX.mm10.36mers.unique.bam -i=G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-ER4-24h-GATA1-Control-Rep2-ENCFF001MSL.mm10.36mers.unique.bam -i=G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.30M.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep2

# Peak calls for for pooled datasets:
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.sorted.bam -i=G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.Control.pooled.sorted.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Pooled
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.ChIP.pooled.sorted.bam -i=G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.Control.pooled.sorted.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Pooled

# Peak calls for for pooled pseudoreplicates:
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.sorted.pseudoRep1.bam -i=G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.Control.pooled.sorted.pseudoRep1.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoRep1
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.sorted.pseudoRep2.bam -i=G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.Control.pooled.sorted.pseudoRep2.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoRep2
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.ChIP.pooled.sorted.pseudoRep1.bam -i=G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.Control.pooled.sorted.pseudoRep1.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-PooledPseudoRep1
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.ChIP.pooled.sorted.pseudoRep2.bam -i=G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.Control.pooled.sorted.pseudoRep2.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-PooledPseudoRep2

# Peak calls for for individual pseudoreplicates:
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-GATA1-Rep1-ENCFF001MOE.mm10.36mers.unique.pseudoRep1.bam -i=G1E-Control-Rep1-ENCFF001MOR.mm10.36mers.unique.pseudoRep1.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep1PseudoRep1
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-GATA1-Rep1-ENCFF001MOE.mm10.36mers.unique.pseudoRep2.bam -i=G1E-Control-Rep1-ENCFF001MOR.mm10.36mers.unique.pseudoRep2.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep1PseudoRep2
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-GATA1-Rep2-ENCFF001MOM.mm10.36mers.unique.pseudoRep1.bam -i=G1E-Control-Rep2-ENCFF001MPG.mm10.36mers.unique.30M.pseudoRep1.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep2PseudoRep1
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-GATA1-Rep2-ENCFF001MOM.mm10.36mers.unique.pseudoRep2.bam -i=G1E-Control-Rep2-ENCFF001MPG.mm10.36mers.unique.30M.pseudoRep2.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep2PseudoRep2
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-ER4-24h-GATA1-Control-Rep1-ENCFF001MRX.mm10.36mers.unique.pseudoRep1.bam -i=G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.pseudoRep1.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1PseudoRep1
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-ER4-24h-GATA1-Control-Rep1-ENCFF001MRX.mm10.36mers.unique.pseudoRep2.bam -i=G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.pseudoRep2.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1PseudoRep2
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-ER4-24h-GATA1-Control-Rep2-ENCFF001MSL.mm10.36mers.unique.pseudoRep1.bam -i=G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.30M.pseudoRep1.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep2PseudoRep1
Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=G1E-ER4-24h-GATA1-Control-Rep2-ENCFF001MSL.mm10.36mers.unique.pseudoRep2.bam -i=G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.30M.pseudoRep2.bam -p=16 -npeak=300000 -savr -savp -rf -odir=SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-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-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep1/G1E-GATA1-Rep1-ENCFF001MOE.mm10.36mers.unique_VS_G1E-Control-Rep1-ENCFF001MOR.mm10.36mers.unique.regionPeak SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep2/G1E-GATA1-Rep2-ENCFF001MOM.mm10.36mers.unique_VS_G1E-Control-Rep2-ENCFF001MPG.mm10.36mers.unique.30M.regionPeak -1 IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1/G1E-ER4-24h-GATA1-Control-Rep1-ENCFF001MRX.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.regionPeak SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep2/G1E-ER4-24h-GATA1-Control-Rep2-ENCFF001MSL.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.30M.regionPeak -1 IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss 0 F signal.value

# IDR for pooled pseudoreplicates:
Rscript batch-consistency-analysis.r SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoRep1/G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.sorted.pseudoRep1_VS_G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoRep2/G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.ChIP.pooled.sorted.pseudoRep2_VS_G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-PooledPseudoRep1/G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.ChIP.pooled.sorted.pseudoRep1_VS_G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-PooledPseudoRep2/G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.ChIP.pooled.sorted.pseudoRep2_VS_G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-PooledPseudoReps 0 F signal.value

# IDR for individual pseudoreplicates:
Rscript batch-consistency-analysis.r SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep1PseudoRep1/G1E-GATA1-Rep1-ENCFF001MOE.mm10.36mers.unique.pseudoRep1_VS_G1E-Control-Rep1-ENCFF001MOR.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep1PseudoRep2/G1E-GATA1-Rep1-ENCFF001MOE.mm10.36mers.unique.pseudoRep2_VS_G1E-Control-Rep1-ENCFF001MOR.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep2PseudoRep1/G1E-GATA1-Rep2-ENCFF001MOM.mm10.36mers.unique.pseudoRep1_VS_G1E-Control-Rep2-ENCFF001MPG.mm10.36mers.unique.30M.pseudoRep1.regionPeak SPP-300K-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep2PseudoRep2/G1E-GATA1-Rep2-ENCFF001MOM.mm10.36mers.unique.pseudoRep2_VS_G1E-Control-Rep2-ENCFF001MPG.mm10.36mers.unique.30M.pseudoRep2.regionPeak -1 IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1PseudoRep1/G1E-ER4-24h-GATA1-Control-Rep1-ENCFF001MRX.mm10.36mers.unique.pseudoRep1_VS_G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1PseudoRep2/G1E-ER4-24h-GATA1-Control-Rep1-ENCFF001MRX.mm10.36mers.unique.pseudoRep2_VS_G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep2PseudoRep1/G1E-ER4-24h-GATA1-Control-Rep2-ENCFF001MSL.mm10.36mers.unique.pseudoRep1_VS_G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.30M.pseudoRep1.regionPeak SPP-300K-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep2PseudoRep2/G1E-ER4-24h-GATA1-Control-Rep2-ENCFF001MSL.mm10.36mers.unique.pseudoRep2_VS_G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.30M.pseudoRep2.regionPeak -1 IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep2PseudoReps 0 F signal.value

# IDR plots for individual replicates:
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss

# IDR plots for pooled pseudoreplicates:
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoReps IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-PooledPseudoReps IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-PooledPseudoReps

# IDR plots individual pseudoreplicates:
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep1PseudoReps IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep2PseudoReps IDR-SPP-G1E-GATA1-ENCFF001MOE-vs-ENCFF001MOM-ss-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1PseudoReps IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep2PseudoReps IDR-SPP-G1E-ER4-24h-GATA1-Control-ENCFF001MRX-vs-ENCFF001MSL-ss-Rep2PseudoReps

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