/oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples GM23338-Oct4-HAIB.dedup.merged.pseudoRep1-SPP-300K/GM23338-Oct4-HAIB.dedup.merged.pseudoRep1_VS_GM23338-Control-HAIB.dedup.merged.pseudoRep1.narrowPeak.gz GM23338-Oct4-HAIB.dedup.merged.pseudoRep2-SPP-300K/GM23338-Oct4-HAIB.dedup.merged.pseudoRep2_VS_GM23338-Control-HAIB.dedup.merged.pseudoRep2.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-GM23338-Oct4-HAIB-pseudoreps --rank q.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
/oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples GM23338-Oct4-HAIB-Rep1-ENCFF647APA.36mers.unique-SPP-300K/GM23338-Oct4-HAIB-Rep1-ENCFF647APA.36mers.unique_VS_GM23338-Control-HAIB-Rep1-ENCFF484RXR.36mers.unique.narrowPeak.gz GM23338-Oct4-HAIB-Rep2-ENCFF986KEK.36mers.unique-SPP-300K/GM23338-Oct4-HAIB-Rep2-ENCFF986KEK.36mers.unique_VS_GM23338-Control-HAIB-Rep2-ENCFF252PYF.36mers.unique.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-GM23338-Oct4-HAIB-indreps --rank q.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
/oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples H1-hESC-Oct4-HAIB.dedup.merged.pseudoRep1-SPP-300K/H1-hESC-Oct4-HAIB.dedup.merged.pseudoRep1_VS_H1-hESC-Control-HAIB.dedup.merged.pseudoRep1.narrowPeak.gz H1-hESC-Oct4-HAIB.dedup.merged.pseudoRep2-SPP-300K/H1-hESC-Oct4-HAIB.dedup.merged.pseudoRep2_VS_H1-hESC-Control-HAIB.dedup.merged.pseudoRep2.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-H1-hESC-Oct4-HAIB-pseudoreps --rank q.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
/oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples H1-hESC-Oct4-HAIB-Rep1-ENCFF000ORV.36mers.unique-SPP-300K/H1-hESC-Oct4-HAIB-Rep1-ENCFF000ORV.36mers.unique_VS_H1-hESC-Control-HAIB-Rep1-ENCFF000OST.36mers.unique.narrowPeak.gz H1-hESC-Oct4-HAIB-Rep2-ENCFF000ORW.36mers.unique-SPP-300K/H1-hESC-Oct4-HAIB-Rep2-ENCFF000ORW.36mers.unique_VS_H1-hESC-Control-HAIB-Rep2-ENCFF000OSS.36mers.unique.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-H1-hESC-Oct4-HAIB-indreps --rank q.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
/oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples K562-Oct4-Snyder.dedup.merged.pseudoRep1-SPP-300K/K562-Oct4-Snyder.dedup.merged.pseudoRep1_VS_K562-Control-Snyder.dedup.merged.pseudoRep1.narrowPeak.gz K562-Oct4-Snyder.dedup.merged.pseudoRep2-SPP-300K/K562-Oct4-Snyder.dedup.merged.pseudoRep2_VS_K562-Control-Snyder.dedup.merged.pseudoRep2.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-K562-Oct4-Snyder-pseudoreps --rank q.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR
/oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples K562-Oct4-Snyder-Rep1-ENCFF002EEN.36mers.unique-SPP-300K/K562-Oct4-Snyder-Rep1-ENCFF002EEN.36mers.unique_VS_K562-Control-Snyder-Rep1-ENCFF002ECS.36mers.unique.narrowPeak.gz K562-Oct4-Snyder-Rep1-ENCFF002EEQ.36mers.unique-SPP-300K/K562-Oct4-Snyder-Rep1-ENCFF002EEQ.36mers.unique_VS_K562-Control-Snyder-Rep1-ENCFF002ECW.36mers.unique.narrowPeak.gz --input-file-type narrowPeak --output-file SPP-IDR-K562-Oct4-Snyder-indreps --rank q.value --soft-idr-threshold 0.05 --plot --use-best-multisummit-IDR