/oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples SPP-300K-CTCF_N4293-ChIP.pseudoRep1.2x75mers-trimmed.bwa-mem.hg19-female.dedup.merged/CTCF_N4293-ChIP.sorted.pseudoRep1_VS_CTCF_N4293-Input.sorted.pseudoRep1.narrowPeak.gz SPP-300K-CTCF_N4293-ChIP.pseudoRep2.2x75mers-trimmed.bwa-mem.hg19-female.dedup.merged/CTCF_N4293-ChIP.sorted.pseudoRep2_VS_CTCF_N4293-Input.sorted.pseudoRep2.narrowPeak.gz --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --peak-list SPP-300K-CTCF_N4293-ChIP.2x75mers-trimmed.bwa-mem.hg19-female.dedup.merged/CTCF_N4293-ChIP.sorted_VS_CTCF_N4293-Input.sorted.narrowPeak.gz --output-file SPP-IDR-CTCF_N4293-ChIP.pseudoReps
/oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples SPP-300K-L119-CRISPRa-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female.dedup/L119-CRISPRa-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female.dedup_VS_L110-CRISPRa-CTCF_N4293-Input.2x75mers-trimmed.bwa-mem.hg19-female.dedup.narrowPeak.gz SPP-300K-L120-CRISPRk-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female.dedup/L120-CRISPRk-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female.dedup_VS_L111-CRISPRk-CTCF_N4293-Input.2x75mers-trimmed.bwa-mem.hg19-female.dedup.narrowPeak.gz --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --peak-list SPP-300K-CTCF_N4293-ChIP.2x75mers-trimmed.bwa-mem.hg19-female.dedup.merged/CTCF_N4293-ChIP.sorted_VS_CTCF_N4293-Input.sorted.narrowPeak.gz --output-file SPP-IDR-CTCF_N4293-ChIP.L119-L120
/oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples SPP-300K-L119-CRISPRa-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female.dedup/L119-CRISPRa-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female.dedup_VS_L110-CRISPRa-CTCF_N4293-Input.2x75mers-trimmed.bwa-mem.hg19-female.dedup.narrowPeak.gz SPP-300K-L130-CRISPRi-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female.dedup/L130-CRISPRi-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female.dedup_VS_L112-CRISPRi-CTCF_N4293-Input.2x75mers-trimmed.bwa-mem.hg19-female.dedup.narrowPeak.gz --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --peak-list SPP-300K-CTCF_N4293-ChIP.2x75mers-trimmed.bwa-mem.hg19-female.dedup.merged/CTCF_N4293-ChIP.sorted_VS_CTCF_N4293-Input.sorted.narrowPeak.gz --output-file SPP-IDR-CTCF_N4293-ChIP.L119-L130
/oak/stanford/groups/akundaje/marinovg/programs/idr-2.0.4/bin/idr --samples SPP-300K-L120-CRISPRk-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female.dedup/L120-CRISPRk-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female.dedup_VS_L111-CRISPRk-CTCF_N4293-Input.2x75mers-trimmed.bwa-mem.hg19-female.dedup.narrowPeak.gz SPP-300K-L130-CRISPRi-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female.dedup/L130-CRISPRi-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female.dedup_VS_L112-CRISPRi-CTCF_N4293-Input.2x75mers-trimmed.bwa-mem.hg19-female.dedup.narrowPeak.gz --input-file-type narrowPeak --rank signal.value --soft-idr-threshold 0.05 --plot --peak-list SPP-300K-CTCF_N4293-ChIP.2x75mers-trimmed.bwa-mem.hg19-female.dedup.merged/CTCF_N4293-ChIP.sorted_VS_CTCF_N4293-Input.sorted.narrowPeak.gz --output-file SPP-IDR-CTCF_N4293-ChIP.L129-L130