# make SPP output folders for individual replicates:
mkdir SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep1
mkdir SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep2
mkdir SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep1
mkdir SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep2
mkdir SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep1
mkdir SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep2
mkdir SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep1
mkdir SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep2
mkdir SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep1
mkdir SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep2
mkdir SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep1
mkdir SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep2
mkdir SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1
mkdir SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2
mkdir SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1
mkdir SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep1
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep2
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep2

# make SPP output folders for pooled runs:
mkdir SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Pooled
mkdir SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Pooled
mkdir SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Pooled
mkdir SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Pooled
mkdir SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled
mkdir SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Pooled
mkdir SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Pooled
mkdir SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Pooled
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Pooled
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Pooled
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Pooled

# make SPP output folders for pooled pseudoreplicates:
mkdir SPP-300K-C2C12_MyoD_24h_10008-vs-10296-PooledPseudoRep1
mkdir SPP-300K-C2C12_MyoD_24h_10008-vs-10296-PooledPseudoRep2
mkdir SPP-300K-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoRep1
mkdir SPP-300K-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoRep2
mkdir SPP-300K-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoRep1
mkdir SPP-300K-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoRep2
mkdir SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-PooledPseudoRep1
mkdir SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-PooledPseudoRep2
mkdir SPP-300K-C2C12-60h-myogenin-16273-vs-16495-PooledPseudoRep1
mkdir SPP-300K-C2C12-60h-myogenin-16273-vs-16495-PooledPseudoRep2
mkdir SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-PooledPseudoRep1
mkdir SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-PooledPseudoRep2
mkdir SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-PooledPseudoRep1
mkdir SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-PooledPseudoRep2
mkdir SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-PooledPseudoRep1
mkdir SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-PooledPseudoRep2
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoRep1
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoRep2
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-PooledPseudoRep1
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-PooledPseudoRep2
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoRep1
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoRep2

# make SPP output folders for individual pseudoreplicates:
mkdir SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep1PseudoRep1
mkdir SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep1PseudoRep2
mkdir SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep2PseudoRep1
mkdir SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep2PseudoRep2
mkdir SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep1PseudoRep1
mkdir SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep1PseudoRep2
mkdir SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep2PseudoRep1
mkdir SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep2PseudoRep2
mkdir SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep1PseudoRep1
mkdir SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep1PseudoRep2
mkdir SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep2PseudoRep1
mkdir SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep2PseudoRep2
mkdir SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep1PseudoRep1
mkdir SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep1PseudoRep2
mkdir SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep2PseudoRep1
mkdir SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep2PseudoRep2
mkdir SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep1PseudoRep1
mkdir SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep1PseudoRep2
mkdir SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep2PseudoRep1
mkdir SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep2PseudoRep2
mkdir SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep1PseudoRep1
mkdir SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep1PseudoRep2
mkdir SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep2PseudoRep1
mkdir SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep2PseudoRep2
mkdir SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1PseudoRep1
mkdir SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1PseudoRep2
mkdir SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2PseudoRep1
mkdir SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2PseudoRep2
mkdir SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1PseudoRep1
mkdir SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1PseudoRep2
mkdir SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2PseudoRep1
mkdir SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2PseudoRep2
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1PseudoRep1
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1PseudoRep2
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2PseudoRep1
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2PseudoRep2
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep1PseudoRep1
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep1PseudoRep2
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep2PseudoRep1
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep2PseudoRep2
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1PseudoRep1
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1PseudoRep2
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep2PseudoRep1
mkdir SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep2PseudoRep2

# merge replicate BAM files:
samtools merge C2C12_MyoD_24h_10008-vs-10296.ChIP.pooled.bam C2C12-24h-MyoD-10008-1pFA.mm10.36mers.unique.bam C2C12-24h-MyoD-10296-1pFA.mm10.36mers.unique.bam
samtools merge C2C12_MyoD_24h_10008-vs-10296.Control.pooled.bam C2C12-24h-2PCR-Input-10007-1pFA.mm10.36mers.unique.bam C2C12-24h-2PCR-Input-10391-1pFA.mm10.36mers.unique.bam
samtools merge C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.bam C2C12-60h-MyoD-60-min-16058.mm10.36mers.unique.bam C2C12-60h-MyoD-75-min-16059.mm10.36mers.unique.bam
samtools merge C2C12-60h-MyoD-16058-vs-16059.Control.pooled.bam C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.bam C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.bam
samtools merge C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.bam C2C12-exp-MyoD-5273-IP-B4-16265.mm10.36mers.unique.bam C2C12-exp-MyoD-5273-IP-C4-16266.mm10.36mers.unique.bam
samtools merge C2C12-exp-MyoD-16265-vs-16266.Control.pooled.bam C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.bam C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.bam
samtools merge C2C12-60h-p300-37C-16274-vs-16507.ChIP.pooled.bam C2C12-myocyte-p300-H3115-37C-5273-IP-B5-5272-16274.mm10.36mers.unique.bam C2C12-60h-p300-37oC-5404-5406-IP-4D-16507.mm10.36mers.unique.bam
samtools merge C2C12-60h-p300-37C-16274-vs-16507.Control.pooled.bam C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.bam C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.bam
samtools merge C2C12-60h-myogenin-16273-vs-16495.ChIP.pooled.bam C2C12-myocyte-myogenin-RT-5273-IP-E4-5261-16273.mm10.36mers.unique.bam C2C12-60h-myogenin-RT-5199-5406-IP-2C-16495.mm10.36mers.unique.bam
samtools merge C2C12-60h-myogenin-16273-vs-16495.Control.pooled.bam C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.bam C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.bam
samtools merge C2C12-exp-p300-37C-16506-vs-16511.ChIP.pooled.bam C2C12-exp-p300-37oC-5271-5406-IP-4C-16506.mm10.36mers.unique.bam C2C12-exp-p300-37oC-6663-5406-IP-5B-16511.mm10.36mers.unique.bam
samtools merge C2C12-exp-p300-37C-16506-vs-16511.Control.pooled.bam C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.bam C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.bam
samtools merge C2C12-60h-MEF2-37C-16272-vs-16504.ChIP.pooled.bam C2C12-myocyte-MEF2-37C-5273-IP-F3-5272-16272.mm10.36mers.unique.bam C2C12-60h-MEF2-B4-37oC-5404-5406-IP-3F-16504.mm10.36mers.unique.bam
samtools merge C2C12-60h-MEF2-37C-16272-vs-16504.Control.pooled.bam C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.bam C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.bam
samtools merge C2C12-60h-Mef2C-37C-16500-vs-16643.ChIP.pooled.bam C2C12-60h-Mef2C-37oC-5404-5406-IP-3B-16500.mm10.36mers.unique.bam C2C12-60h-Mef2C-H180-37oC-5453-IP-C2-16643.mm10.36mers.unique.bam
samtools merge C2C12-60h-Mef2C-37C-16500-vs-16643.Control.pooled.bam C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.bam C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.bam
samtools merge C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.bam C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.bam C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.bam
samtools merge C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.bam C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam
samtools merge C2C12-exp-MEF2-B4-37C-16502-vs-16645.ChIP.pooled.bam C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.bam C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.bam
samtools merge C2C12-exp-MEF2-B4-37C-16502-vs-16645.Control.pooled.bam C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam
samtools merge C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.bam C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.bam C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.bam
samtools merge C2C12-exp-MEF2-B4-37C-16503-vs-16645.Control.pooled.bam C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam

# sort merged BAM files:
samtools sort C2C12_MyoD_24h_10008-vs-10296.ChIP.pooled.bam C2C12_MyoD_24h_10008-vs-10296.ChIP.pooled.sorted
samtools sort C2C12_MyoD_24h_10008-vs-10296.Control.pooled.bam C2C12_MyoD_24h_10008-vs-10296.Control.pooled.sorted
samtools sort C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.bam C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.sorted
samtools sort C2C12-60h-MyoD-16058-vs-16059.Control.pooled.bam C2C12-60h-MyoD-16058-vs-16059.Control.pooled.sorted
samtools sort C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.bam C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.sorted
samtools sort C2C12-exp-MyoD-16265-vs-16266.Control.pooled.bam C2C12-exp-MyoD-16265-vs-16266.Control.pooled.sorted
samtools sort C2C12-60h-p300-37C-16274-vs-16507.ChIP.pooled.bam C2C12-60h-p300-37C-16274-vs-16507.ChIP.pooled.sorted
samtools sort C2C12-60h-p300-37C-16274-vs-16507.Control.pooled.bam C2C12-60h-p300-37C-16274-vs-16507.Control.pooled.sorted
samtools sort C2C12-60h-myogenin-16273-vs-16495.ChIP.pooled.bam C2C12-60h-myogenin-16273-vs-16495.ChIP.pooled.sorted
samtools sort C2C12-60h-myogenin-16273-vs-16495.Control.pooled.bam C2C12-60h-myogenin-16273-vs-16495.Control.pooled.sorted
samtools sort C2C12-exp-p300-37C-16506-vs-16511.ChIP.pooled.bam C2C12-exp-p300-37C-16506-vs-16511.ChIP.pooled.sorted
samtools sort C2C12-exp-p300-37C-16506-vs-16511.Control.pooled.bam C2C12-exp-p300-37C-16506-vs-16511.Control.pooled.sorted
samtools sort C2C12-60h-MEF2-37C-16272-vs-16504.ChIP.pooled.bam C2C12-60h-MEF2-37C-16272-vs-16504.ChIP.pooled.sorted
samtools sort C2C12-60h-MEF2-37C-16272-vs-16504.Control.pooled.bam C2C12-60h-MEF2-37C-16272-vs-16504.Control.pooled.sorted
samtools sort C2C12-60h-Mef2C-37C-16500-vs-16643.ChIP.pooled.bam C2C12-60h-Mef2C-37C-16500-vs-16643.ChIP.pooled.sorted
samtools sort C2C12-60h-Mef2C-37C-16500-vs-16643.Control.pooled.bam C2C12-60h-Mef2C-37C-16500-vs-16643.Control.pooled.sorted
samtools sort C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.bam C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.sorted
samtools sort C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.bam C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.sorted
samtools sort C2C12-exp-MEF2-B4-37C-16502-vs-16645.ChIP.pooled.bam C2C12-exp-MEF2-B4-37C-16502-vs-16645.ChIP.pooled.sorted
samtools sort C2C12-exp-MEF2-B4-37C-16502-vs-16645.Control.pooled.bam C2C12-exp-MEF2-B4-37C-16502-vs-16645.Control.pooled.sorted
samtools sort C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.bam C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.sorted
samtools sort C2C12-exp-MEF2-B4-37C-16503-vs-16645.Control.pooled.bam C2C12-exp-MEF2-B4-37C-16503-vs-16645.Control.pooled.sorted

# index sorted BAM files:
samtools index C2C12_MyoD_24h_10008-vs-10296.ChIP.pooled.sorted.bam
samtools index C2C12_MyoD_24h_10008-vs-10296.Control.pooled.sorted.bam
samtools index C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.sorted.bam
samtools index C2C12-60h-MyoD-16058-vs-16059.Control.pooled.sorted.bam
samtools index C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.sorted.bam
samtools index C2C12-exp-MyoD-16265-vs-16266.Control.pooled.sorted.bam
samtools index C2C12-60h-p300-37C-16274-vs-16507.ChIP.pooled.sorted.bam
samtools index C2C12-60h-p300-37C-16274-vs-16507.Control.pooled.sorted.bam
samtools index C2C12-60h-myogenin-16273-vs-16495.ChIP.pooled.sorted.bam
samtools index C2C12-60h-myogenin-16273-vs-16495.Control.pooled.sorted.bam
samtools index C2C12-exp-p300-37C-16506-vs-16511.ChIP.pooled.sorted.bam
samtools index C2C12-exp-p300-37C-16506-vs-16511.Control.pooled.sorted.bam
samtools index C2C12-60h-MEF2-37C-16272-vs-16504.ChIP.pooled.sorted.bam
samtools index C2C12-60h-MEF2-37C-16272-vs-16504.Control.pooled.sorted.bam
samtools index C2C12-60h-Mef2C-37C-16500-vs-16643.ChIP.pooled.sorted.bam
samtools index C2C12-60h-Mef2C-37C-16500-vs-16643.Control.pooled.sorted.bam
samtools index C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.sorted.bam
samtools index C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.sorted.bam
samtools index C2C12-exp-MEF2-B4-37C-16502-vs-16645.ChIP.pooled.sorted.bam
samtools index C2C12-exp-MEF2-B4-37C-16502-vs-16645.Control.pooled.sorted.bam
samtools index C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.sorted.bam
samtools index C2C12-exp-MEF2-B4-37C-16503-vs-16645.Control.pooled.sorted.bam

# Generate pseudoreplicates:
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12_MyoD_24h_10008-vs-10296.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12_MyoD_24h_10008-vs-10296.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-24h-MyoD-10008-1pFA.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-24h-MyoD-10296-1pFA.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-24h-2PCR-Input-10007-1pFA.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-24h-2PCR-Input-10391-1pFA.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-MyoD-16058-vs-16059.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-MyoD-60-min-16058.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-MyoD-75-min-16059.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MyoD-16265-vs-16266.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MyoD-5273-IP-B4-16265.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MyoD-5273-IP-C4-16266.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-p300-37C-16274-vs-16507.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-p300-37C-16274-vs-16507.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-myocyte-p300-H3115-37C-5273-IP-B5-5272-16274.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-p300-37oC-5404-5406-IP-4D-16507.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-myogenin-16273-vs-16495.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-myogenin-16273-vs-16495.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-myocyte-myogenin-RT-5273-IP-E4-5261-16273.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-myogenin-RT-5199-5406-IP-2C-16495.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-p300-37C-16506-vs-16511.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-p300-37C-16506-vs-16511.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-p300-37oC-5271-5406-IP-4C-16506.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-p300-37oC-6663-5406-IP-5B-16511.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-MEF2-37C-16272-vs-16504.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-MEF2-37C-16272-vs-16504.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-myocyte-MEF2-37C-5273-IP-F3-5272-16272.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-MEF2-B4-37oC-5404-5406-IP-3F-16504.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-Mef2C-37C-16500-vs-16643.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-Mef2C-37C-16500-vs-16643.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-Mef2C-37oC-5404-5406-IP-3B-16500.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-Mef2C-H180-37oC-5453-IP-C2-16643.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MEF2-B4-37C-16502-vs-16645.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MEF2-B4-37C-16502-vs-16645.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MEF2-B4-37C-16503-vs-16645.Control.pooled.sorted.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam
python /woldlab/castor/home/georgi/code-new/BAMPseudoReps.py C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam

# Peak calls for individual replicates:
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-24h-MyoD-10008-1pFA.mm10.36mers.unique.bam -i=C2C12-24h-2PCR-Input-10007-1pFA.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-24h-MyoD-10296-1pFA.mm10.36mers.unique.bam -i=C2C12-24h-2PCR-Input-10391-1pFA.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MyoD-60-min-16058.mm10.36mers.unique.bam -i=C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MyoD-75-min-16059.mm10.36mers.unique.bam -i=C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MyoD-5273-IP-B4-16265.mm10.36mers.unique.bam -i=C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MyoD-5273-IP-C4-16266.mm10.36mers.unique.bam -i=C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-myocyte-p300-H3115-37C-5273-IP-B5-5272-16274.mm10.36mers.unique.bam -i=C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-p300-37oC-5404-5406-IP-4D-16507.mm10.36mers.unique.bam -i=C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-myocyte-myogenin-RT-5273-IP-E4-5261-16273.mm10.36mers.unique.bam -i=C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-myogenin-RT-5199-5406-IP-2C-16495.mm10.36mers.unique.bam -i=C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-p300-37oC-5271-5406-IP-4C-16506.mm10.36mers.unique.bam -i=C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-p300-37oC-6663-5406-IP-5B-16511.mm10.36mers.unique.bam -i=C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-myocyte-MEF2-37C-5273-IP-F3-5272-16272.mm10.36mers.unique.bam -i=C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MEF2-B4-37oC-5404-5406-IP-3F-16504.mm10.36mers.unique.bam -i=C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-Mef2C-37oC-5404-5406-IP-3B-16500.mm10.36mers.unique.bam -i=C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-Mef2C-H180-37oC-5453-IP-C2-16643.mm10.36mers.unique.bam -i=C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep2

# Peak calls for for pooled datasets:
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12_MyoD_24h_10008-vs-10296.ChIP.pooled.sorted.bam -i=C2C12_MyoD_24h_10008-vs-10296.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Pooled
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.sorted.bam -i=C2C12-60h-MyoD-16058-vs-16059.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Pooled
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.sorted.bam -i=C2C12-exp-MyoD-16265-vs-16266.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Pooled
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-p300-37C-16274-vs-16507.ChIP.pooled.sorted.bam -i=C2C12-60h-p300-37C-16274-vs-16507.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Pooled
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-myogenin-16273-vs-16495.ChIP.pooled.sorted.bam -i=C2C12-60h-myogenin-16273-vs-16495.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Pooled
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-p300-37C-16506-vs-16511.ChIP.pooled.sorted.bam -i=C2C12-exp-p300-37C-16506-vs-16511.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Pooled
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MEF2-37C-16272-vs-16504.ChIP.pooled.sorted.bam -i=C2C12-60h-MEF2-37C-16272-vs-16504.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Pooled
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-Mef2C-37C-16500-vs-16643.ChIP.pooled.sorted.bam -i=C2C12-60h-Mef2C-37C-16500-vs-16643.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Pooled
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.sorted.bam -i=C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Pooled
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37C-16502-vs-16645.ChIP.pooled.sorted.bam -i=C2C12-exp-MEF2-B4-37C-16502-vs-16645.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Pooled
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.sorted.bam -i=C2C12-exp-MEF2-B4-37C-16503-vs-16645.Control.pooled.sorted.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Pooled

# Peak calls for for pooled pseudoreplicates:
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12_MyoD_24h_10008-vs-10296.ChIP.pooled.sorted.pseudoRep1.bam -i=C2C12_MyoD_24h_10008-vs-10296.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12_MyoD_24h_10008-vs-10296-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12_MyoD_24h_10008-vs-10296.ChIP.pooled.sorted.pseudoRep2.bam -i=C2C12_MyoD_24h_10008-vs-10296.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12_MyoD_24h_10008-vs-10296-PooledPseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.sorted.pseudoRep1.bam -i=C2C12-60h-MyoD-16058-vs-16059.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.sorted.pseudoRep2.bam -i=C2C12-60h-MyoD-16058-vs-16059.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.sorted.pseudoRep1.bam -i=C2C12-exp-MyoD-16265-vs-16266.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.sorted.pseudoRep2.bam -i=C2C12-exp-MyoD-16265-vs-16266.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-p300-37C-16274-vs-16507.ChIP.pooled.sorted.pseudoRep1.bam -i=C2C12-60h-p300-37C-16274-vs-16507.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-p300-37C-16274-vs-16507.ChIP.pooled.sorted.pseudoRep2.bam -i=C2C12-60h-p300-37C-16274-vs-16507.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-PooledPseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-myogenin-16273-vs-16495.ChIP.pooled.sorted.pseudoRep1.bam -i=C2C12-60h-myogenin-16273-vs-16495.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-myogenin-16273-vs-16495-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-myogenin-16273-vs-16495.ChIP.pooled.sorted.pseudoRep2.bam -i=C2C12-60h-myogenin-16273-vs-16495.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-myogenin-16273-vs-16495-PooledPseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-p300-37C-16506-vs-16511.ChIP.pooled.sorted.pseudoRep1.bam -i=C2C12-exp-p300-37C-16506-vs-16511.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-p300-37C-16506-vs-16511.ChIP.pooled.sorted.pseudoRep2.bam -i=C2C12-exp-p300-37C-16506-vs-16511.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-PooledPseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MEF2-37C-16272-vs-16504.ChIP.pooled.sorted.pseudoRep1.bam -i=C2C12-60h-MEF2-37C-16272-vs-16504.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MEF2-37C-16272-vs-16504.ChIP.pooled.sorted.pseudoRep2.bam -i=C2C12-60h-MEF2-37C-16272-vs-16504.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-PooledPseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-Mef2C-37C-16500-vs-16643.ChIP.pooled.sorted.pseudoRep1.bam -i=C2C12-60h-Mef2C-37C-16500-vs-16643.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-Mef2C-37C-16500-vs-16643.ChIP.pooled.sorted.pseudoRep2.bam -i=C2C12-60h-Mef2C-37C-16500-vs-16643.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-PooledPseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.sorted.pseudoRep1.bam -i=C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.sorted.pseudoRep2.bam -i=C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37C-16502-vs-16645.ChIP.pooled.sorted.pseudoRep1.bam -i=C2C12-exp-MEF2-B4-37C-16502-vs-16645.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37C-16502-vs-16645.ChIP.pooled.sorted.pseudoRep2.bam -i=C2C12-exp-MEF2-B4-37C-16502-vs-16645.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-PooledPseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.sorted.pseudoRep1.bam -i=C2C12-exp-MEF2-B4-37C-16503-vs-16645.Control.pooled.sorted.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.sorted.pseudoRep2.bam -i=C2C12-exp-MEF2-B4-37C-16503-vs-16645.Control.pooled.sorted.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoRep2

# Peak calls for for individual pseudoreplicates:
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-24h-MyoD-10008-1pFA.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-24h-2PCR-Input-10007-1pFA.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-24h-MyoD-10008-1pFA.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-24h-2PCR-Input-10007-1pFA.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-24h-MyoD-10296-1pFA.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-24h-2PCR-Input-10391-1pFA.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-24h-MyoD-10296-1pFA.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-24h-2PCR-Input-10391-1pFA.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep2PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MyoD-60-min-16058.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MyoD-60-min-16058.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MyoD-75-min-16059.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MyoD-75-min-16059.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep2PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MyoD-5273-IP-B4-16265.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MyoD-5273-IP-B4-16265.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MyoD-5273-IP-C4-16266.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MyoD-5273-IP-C4-16266.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep2PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-myocyte-p300-H3115-37C-5273-IP-B5-5272-16274.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-myocyte-p300-H3115-37C-5273-IP-B5-5272-16274.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-p300-37oC-5404-5406-IP-4D-16507.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-p300-37oC-5404-5406-IP-4D-16507.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep2PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-myocyte-myogenin-RT-5273-IP-E4-5261-16273.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-myocyte-myogenin-RT-5273-IP-E4-5261-16273.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-myogenin-RT-5199-5406-IP-2C-16495.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-myogenin-RT-5199-5406-IP-2C-16495.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep2PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-p300-37oC-5271-5406-IP-4C-16506.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-p300-37oC-5271-5406-IP-4C-16506.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-p300-37oC-6663-5406-IP-5B-16511.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-p300-37oC-6663-5406-IP-5B-16511.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep2PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-myocyte-MEF2-37C-5273-IP-F3-5272-16272.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-myocyte-MEF2-37C-5273-IP-F3-5272-16272.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MEF2-B4-37oC-5404-5406-IP-3F-16504.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-MEF2-B4-37oC-5404-5406-IP-3F-16504.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-Mef2C-37oC-5404-5406-IP-3B-16500.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-Mef2C-37oC-5404-5406-IP-3B-16500.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-Mef2C-H180-37oC-5453-IP-C2-16643.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-60h-Mef2C-H180-37oC-5453-IP-C2-16643.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep2PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1PseudoRep2
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.pseudoRep1.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep1.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep2PseudoRep1
Rscript /woldlab/castor/home/georgi/code/spp/spp_package/run_spp.R -c=C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.pseudoRep2.bam -i=C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep2.bam -p=8 -npeak=300000 -savr -savp -rf -odir=SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-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-C2C12_MyoD_24h_10008-vs-10296-Rep1/C2C12-24h-MyoD-10008-1pFA.mm10.36mers.unique_VS_C2C12-24h-2PCR-Input-10007-1pFA.mm10.36mers.unique.regionPeak SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep2/C2C12-24h-MyoD-10296-1pFA.mm10.36mers.unique_VS_C2C12-24h-2PCR-Input-10391-1pFA.mm10.36mers.unique.regionPeak -1 IDR-SPP-C2C12_MyoD_24h_10008-vs-10296 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep1/C2C12-60h-MyoD-60-min-16058.mm10.36mers.unique_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.regionPeak SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep2/C2C12-60h-MyoD-75-min-16059.mm10.36mers.unique_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.regionPeak -1 IDR-SPP-C2C12-60h-MyoD-16058-vs-16059 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep1/C2C12-exp-MyoD-5273-IP-B4-16265.mm10.36mers.unique_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.regionPeak SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep2/C2C12-exp-MyoD-5273-IP-C4-16266.mm10.36mers.unique_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.regionPeak -1 IDR-SPP-C2C12-exp-MyoD-16265-vs-16266 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep1/C2C12-myocyte-p300-H3115-37C-5273-IP-B5-5272-16274.mm10.36mers.unique_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.regionPeak SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep2/C2C12-60h-p300-37oC-5404-5406-IP-4D-16507.mm10.36mers.unique_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.regionPeak -1 IDR-SPP-C2C12-60h-p300-37C-16274-vs-16507 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep1/C2C12-myocyte-myogenin-RT-5273-IP-E4-5261-16273.mm10.36mers.unique_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.regionPeak SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep2/C2C12-60h-myogenin-RT-5199-5406-IP-2C-16495.mm10.36mers.unique_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.regionPeak -1 IDR-SPP-C2C12-60h-myogenin-16273-vs-16495 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep1/C2C12-exp-p300-37oC-5271-5406-IP-4C-16506.mm10.36mers.unique_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.regionPeak SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep2/C2C12-exp-p300-37oC-6663-5406-IP-5B-16511.mm10.36mers.unique_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.regionPeak -1 IDR-SPP-C2C12-exp-p300-37C-16506-vs-16511 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1/C2C12-myocyte-MEF2-37C-5273-IP-F3-5272-16272.mm10.36mers.unique_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.regionPeak SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2/C2C12-60h-MEF2-B4-37oC-5404-5406-IP-3F-16504.mm10.36mers.unique_VS_C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.regionPeak -1 IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1/C2C12-60h-Mef2C-37oC-5404-5406-IP-3B-16500.mm10.36mers.unique_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.regionPeak SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2/C2C12-60h-Mef2C-H180-37oC-5453-IP-C2-16643.mm10.36mers.unique_VS_C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.regionPeak -1 IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1/C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.regionPeak SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2/C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.regionPeak -1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep1/C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.regionPeak SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep2/C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.regionPeak -1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16645 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1/C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.regionPeak SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep2/C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.regionPeak -1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645 0 F signal.value

# IDR for pooled pseudoreplicates:
Rscript batch-consistency-analysis.r SPP-300K-C2C12_MyoD_24h_10008-vs-10296-PooledPseudoRep1/C2C12_MyoD_24h_10008-vs-10296.ChIP.pooled.sorted.pseudoRep1_VS_C2C12_MyoD_24h_10008-vs-10296.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-C2C12_MyoD_24h_10008-vs-10296-PooledPseudoRep2/C2C12_MyoD_24h_10008-vs-10296.ChIP.pooled.sorted.pseudoRep2_VS_C2C12_MyoD_24h_10008-vs-10296.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-C2C12_MyoD_24h_10008-vs-10296-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoRep1/C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-60h-MyoD-16058-vs-16059.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoRep2/C2C12-60h-MyoD-16058-vs-16059.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-60h-MyoD-16058-vs-16059.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoRep1/C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-exp-MyoD-16265-vs-16266.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoRep2/C2C12-exp-MyoD-16265-vs-16266.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-exp-MyoD-16265-vs-16266.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-PooledPseudoRep1/C2C12-60h-p300-37C-16274-vs-16507.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-60h-p300-37C-16274-vs-16507.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-PooledPseudoRep2/C2C12-60h-p300-37C-16274-vs-16507.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-60h-p300-37C-16274-vs-16507.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-p300-37C-16274-vs-16507-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-myogenin-16273-vs-16495-PooledPseudoRep1/C2C12-60h-myogenin-16273-vs-16495.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-60h-myogenin-16273-vs-16495.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-C2C12-60h-myogenin-16273-vs-16495-PooledPseudoRep2/C2C12-60h-myogenin-16273-vs-16495.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-60h-myogenin-16273-vs-16495.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-myogenin-16273-vs-16495-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-PooledPseudoRep1/C2C12-exp-p300-37C-16506-vs-16511.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-exp-p300-37C-16506-vs-16511.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-PooledPseudoRep2/C2C12-exp-p300-37C-16506-vs-16511.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-exp-p300-37C-16506-vs-16511.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-p300-37C-16506-vs-16511-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-PooledPseudoRep1/C2C12-60h-MEF2-37C-16272-vs-16504.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-60h-MEF2-37C-16272-vs-16504.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-PooledPseudoRep2/C2C12-60h-MEF2-37C-16272-vs-16504.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-60h-MEF2-37C-16272-vs-16504.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-PooledPseudoRep1/C2C12-60h-Mef2C-37C-16500-vs-16643.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-60h-Mef2C-37C-16500-vs-16643.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-PooledPseudoRep2/C2C12-60h-Mef2C-37C-16500-vs-16643.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-60h-Mef2C-37C-16500-vs-16643.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoRep1/C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoRep2/C2C12-exp-MEF2-B4-37C-16502-vs-16503.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-exp-MEF2-B4-37C-16502-vs-16503.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-PooledPseudoRep1/C2C12-exp-MEF2-B4-37C-16502-vs-16645.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-exp-MEF2-B4-37C-16502-vs-16645.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-PooledPseudoRep2/C2C12-exp-MEF2-B4-37C-16502-vs-16645.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-exp-MEF2-B4-37C-16502-vs-16645.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16645-PooledPseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoRep1/C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.sorted.pseudoRep1_VS_C2C12-exp-MEF2-B4-37C-16503-vs-16645.Control.pooled.sorted.pseudoRep1.regionPeak SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoRep2/C2C12-exp-MEF2-B4-37C-16503-vs-16645.ChIP.pooled.sorted.pseudoRep2_VS_C2C12-exp-MEF2-B4-37C-16503-vs-16645.Control.pooled.sorted.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoReps 0 F signal.value

# IDR for individual pseudoreplicates:
Rscript batch-consistency-analysis.r SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep1PseudoRep1/C2C12-24h-MyoD-10008-1pFA.mm10.36mers.unique.pseudoRep1_VS_C2C12-24h-2PCR-Input-10007-1pFA.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep1PseudoRep2/C2C12-24h-MyoD-10008-1pFA.mm10.36mers.unique.pseudoRep2_VS_C2C12-24h-2PCR-Input-10007-1pFA.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12_MyoD_24h_10008-vs-10296-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep2PseudoRep1/C2C12-24h-MyoD-10296-1pFA.mm10.36mers.unique.pseudoRep1_VS_C2C12-24h-2PCR-Input-10391-1pFA.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12_MyoD_24h_10008-vs-10296-Rep2PseudoRep2/C2C12-24h-MyoD-10296-1pFA.mm10.36mers.unique.pseudoRep2_VS_C2C12-24h-2PCR-Input-10391-1pFA.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12_MyoD_24h_10008-vs-10296-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep1PseudoRep1/C2C12-60h-MyoD-60-min-16058.mm10.36mers.unique.pseudoRep1_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep1PseudoRep2/C2C12-60h-MyoD-60-min-16058.mm10.36mers.unique.pseudoRep2_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep2PseudoRep1/C2C12-60h-MyoD-75-min-16059.mm10.36mers.unique.pseudoRep1_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-60h-MyoD-16058-vs-16059-Rep2PseudoRep2/C2C12-60h-MyoD-75-min-16059.mm10.36mers.unique.pseudoRep2_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep1PseudoRep1/C2C12-exp-MyoD-5273-IP-B4-16265.mm10.36mers.unique.pseudoRep1_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep1PseudoRep2/C2C12-exp-MyoD-5273-IP-B4-16265.mm10.36mers.unique.pseudoRep2_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-MyoD-16265-vs-16266-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep2PseudoRep1/C2C12-exp-MyoD-5273-IP-C4-16266.mm10.36mers.unique.pseudoRep1_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-exp-MyoD-16265-vs-16266-Rep2PseudoRep2/C2C12-exp-MyoD-5273-IP-C4-16266.mm10.36mers.unique.pseudoRep2_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-MyoD-16265-vs-16266-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep1PseudoRep1/C2C12-myocyte-p300-H3115-37C-5273-IP-B5-5272-16274.mm10.36mers.unique.pseudoRep1_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep1PseudoRep2/C2C12-myocyte-p300-H3115-37C-5273-IP-B5-5272-16274.mm10.36mers.unique.pseudoRep2_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-p300-37C-16274-vs-16507-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep2PseudoRep1/C2C12-60h-p300-37oC-5404-5406-IP-4D-16507.mm10.36mers.unique.pseudoRep1_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-60h-p300-37C-16274-vs-16507-Rep2PseudoRep2/C2C12-60h-p300-37oC-5404-5406-IP-4D-16507.mm10.36mers.unique.pseudoRep2_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-p300-37C-16274-vs-16507-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep1PseudoRep1/C2C12-myocyte-myogenin-RT-5273-IP-E4-5261-16273.mm10.36mers.unique.pseudoRep1_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep1PseudoRep2/C2C12-myocyte-myogenin-RT-5273-IP-E4-5261-16273.mm10.36mers.unique.pseudoRep2_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-myogenin-16273-vs-16495-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep2PseudoRep1/C2C12-60h-myogenin-RT-5199-5406-IP-2C-16495.mm10.36mers.unique.pseudoRep1_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-60h-myogenin-16273-vs-16495-Rep2PseudoRep2/C2C12-60h-myogenin-RT-5199-5406-IP-2C-16495.mm10.36mers.unique.pseudoRep2_VS_C2C12-60h-1PCR-Input-60min-16057.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-myogenin-16273-vs-16495-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep1PseudoRep1/C2C12-exp-p300-37oC-5271-5406-IP-4C-16506.mm10.36mers.unique.pseudoRep1_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep1PseudoRep2/C2C12-exp-p300-37oC-5271-5406-IP-4C-16506.mm10.36mers.unique.pseudoRep2_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-p300-37C-16506-vs-16511-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep2PseudoRep1/C2C12-exp-p300-37oC-6663-5406-IP-5B-16511.mm10.36mers.unique.pseudoRep1_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-exp-p300-37C-16506-vs-16511-Rep2PseudoRep2/C2C12-exp-p300-37oC-6663-5406-IP-5B-16511.mm10.36mers.unique.pseudoRep2_VS_C2C12-myoblast-1PCR-Input-RT-5273-IN-4-5269-16271.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-p300-37C-16506-vs-16511-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1PseudoRep1/C2C12-myocyte-MEF2-37C-5273-IP-F3-5272-16272.mm10.36mers.unique.pseudoRep1_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1PseudoRep2/C2C12-myocyte-MEF2-37C-5273-IP-F3-5272-16272.mm10.36mers.unique.pseudoRep2_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2PseudoRep1/C2C12-60h-MEF2-B4-37oC-5404-5406-IP-3F-16504.mm10.36mers.unique.pseudoRep1_VS_C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2PseudoRep2/C2C12-60h-MEF2-B4-37oC-5404-5406-IP-3F-16504.mm10.36mers.unique.pseudoRep2_VS_C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1PseudoRep1/C2C12-60h-Mef2C-37oC-5404-5406-IP-3B-16500.mm10.36mers.unique.pseudoRep1_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1PseudoRep2/C2C12-60h-Mef2C-37oC-5404-5406-IP-3B-16500.mm10.36mers.unique.pseudoRep2_VS_C2C12-myocyte-1PCR-Input-37C-5273-IN-3-5272-16270.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2PseudoRep1/C2C12-60h-Mef2C-H180-37oC-5453-IP-C2-16643.mm10.36mers.unique.pseudoRep1_VS_C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2PseudoRep2/C2C12-60h-Mef2C-H180-37oC-5453-IP-C2-16643.mm10.36mers.unique.pseudoRep2_VS_C2C12-60h-37oC-1PCR-Input-5406-IN-2-16647.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1PseudoRep1/C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.pseudoRep1_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1PseudoRep2/C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.pseudoRep2_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2PseudoRep1/C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.pseudoRep1_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2PseudoRep2/C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.pseudoRep2_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep1PseudoRep1/C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.pseudoRep1_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep1PseudoRep2/C2C12-exp-MEF2-B4-37oC-5409-5406-IP-3D-16502.mm10.36mers.unique.pseudoRep2_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep2PseudoRep1/C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.pseudoRep1_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep2PseudoRep2/C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.pseudoRep2_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep2PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1PseudoRep1/C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.pseudoRep1_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1PseudoRep2/C2C12-exp-MEF2-B4-37oC-5271-5406-IP-3E-16503.mm10.36mers.unique.pseudoRep2_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1PseudoReps 0 F signal.value
Rscript batch-consistency-analysis.r SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep2PseudoRep1/C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.pseudoRep1_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep1.regionPeak SPP-300K-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep2PseudoRep2/C2C12-exp-Mef2-B4-37oC-5453-IP-E2-16645.mm10.36mers.unique.pseudoRep2_VS_C2C12-exp-37oC-1PCR-Input-5273-IN-5-16646.mm10.36mers.unique.pseudoRep2.regionPeak -1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep2PseudoReps 0 F signal.value

# IDR plots for individual replicates:
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12_MyoD_24h_10008-vs-10296 IDR-SPP-C2C12_MyoD_24h_10008-vs-10296
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-MyoD-16058-vs-16059 IDR-SPP-C2C12-60h-MyoD-16058-vs-16059
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MyoD-16265-vs-16266 IDR-SPP-C2C12-exp-MyoD-16265-vs-16266
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-p300-37C-16274-vs-16507 IDR-SPP-C2C12-60h-p300-37C-16274-vs-16507
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-myogenin-16273-vs-16495 IDR-SPP-C2C12-60h-myogenin-16273-vs-16495
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-p300-37C-16506-vs-16511 IDR-SPP-C2C12-exp-p300-37C-16506-vs-16511
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504 IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643 IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16645 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16645
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645 IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645

# IDR plots for pooled pseudoreplicates:
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12_MyoD_24h_10008-vs-10296-PooledPseudoReps IDR-SPP-C2C12_MyoD_24h_10008-vs-10296-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoReps IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoReps IDR-SPP-C2C12-exp-MyoD-16265-vs-16266-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-p300-37C-16274-vs-16507-PooledPseudoReps IDR-SPP-C2C12-60h-p300-37C-16274-vs-16507-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-myogenin-16273-vs-16495-PooledPseudoReps IDR-SPP-C2C12-60h-myogenin-16273-vs-16495-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-p300-37C-16506-vs-16511-PooledPseudoReps IDR-SPP-C2C12-exp-p300-37C-16506-vs-16511-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504-PooledPseudoReps IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643-PooledPseudoReps IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoReps IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16645-PooledPseudoReps IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16645-PooledPseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoReps IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645-PooledPseudoReps

# IDR plots individual pseudoreplicates:
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12_MyoD_24h_10008-vs-10296-Rep1PseudoReps IDR-SPP-C2C12_MyoD_24h_10008-vs-10296-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12_MyoD_24h_10008-vs-10296-Rep2PseudoReps IDR-SPP-C2C12_MyoD_24h_10008-vs-10296-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-Rep1PseudoReps IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-Rep2PseudoReps IDR-SPP-C2C12-60h-MyoD-16058-vs-16059-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MyoD-16265-vs-16266-Rep1PseudoReps IDR-SPP-C2C12-exp-MyoD-16265-vs-16266-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MyoD-16265-vs-16266-Rep2PseudoReps IDR-SPP-C2C12-exp-MyoD-16265-vs-16266-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-p300-37C-16274-vs-16507-Rep1PseudoReps IDR-SPP-C2C12-60h-p300-37C-16274-vs-16507-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-p300-37C-16274-vs-16507-Rep2PseudoReps IDR-SPP-C2C12-60h-p300-37C-16274-vs-16507-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-myogenin-16273-vs-16495-Rep1PseudoReps IDR-SPP-C2C12-60h-myogenin-16273-vs-16495-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-myogenin-16273-vs-16495-Rep2PseudoReps IDR-SPP-C2C12-60h-myogenin-16273-vs-16495-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-p300-37C-16506-vs-16511-Rep1PseudoReps IDR-SPP-C2C12-exp-p300-37C-16506-vs-16511-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-p300-37C-16506-vs-16511-Rep2PseudoReps IDR-SPP-C2C12-exp-p300-37C-16506-vs-16511-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1PseudoReps IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2PseudoReps IDR-SPP-C2C12-60h-MEF2-37C-16272-vs-16504-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1PseudoReps IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2PseudoReps IDR-SPP-C2C12-60h-Mef2C-37C-16500-vs-16643-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1PseudoReps IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2PseudoReps IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16503-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep1PseudoReps IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep2PseudoReps IDR-SPP-C2C12-exp-MEF2-B4-37C-16502-vs-16645-Rep2PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1PseudoReps IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep1PseudoReps
Rscript batch-consistency-plot.r 1 IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep2PseudoReps IDR-SPP-C2C12-exp-MEF2-B4-37C-16503-vs-16645-Rep2PseudoReps

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