java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_HS_i5006_DY330_rep1_19786.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_HS_i5006_DY330_rep1_19786.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_HS_i5006_DY330_rep2_20238.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_HS_i5006_DY330_rep2_20238.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_MHS_i5006_DY330_rep1_19780.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_MHS_i5006_DY330_rep1_19780.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_MHS_i5006_DY330_rep1_20234.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/Fis_MHS_i5006_DY330_rep1_20234.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep1_20227.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep1_20227.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep2_20228.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep2_20228.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep3_21327.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_HS_i5006_DY330_rep3_21327.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep1_20219.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep1_20219.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep2_20220.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep2_20220.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep3_21320.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/HimD_MHS_i5006_DY330_rep3_21320.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_HS_i5006_DY330_rep1_17259.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_HS_i5006_DY330_rep1_17259.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_HS_i5006_DY330_rep2_17274.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_HS_i5006_DY330_rep2_17274.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_MHS_i5006_DY330_rep1_17251.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_MHS_i5006_DY330_rep1_17251.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_MHS_i5006_DY330_rep2_17267.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/MglB_MHS_i5006_DY330_rep2_17267.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep1_19790.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep1_19790.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep2_20240.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep2_20240.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep3_21307.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_HS_i5006_DY330_rep3_21307.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep1_19784.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep1_19784.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep2_20236.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep2_20236.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep3_21299.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoA_MHS_i5006_DY330_rep3_21299.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep1_17260.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep1_17260.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep2_17275.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep2_17275.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep3_21322.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_HS_i5006_DY330_rep3_21322.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep1_17252.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep1_17252.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep2_17268.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep2_17268.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep3_21315.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoB_MHS_i5006_DY330_rep3_21315.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep1_20231.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep1_20231.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep2_20232.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep2_20232.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep3_21323.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep3_21323.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep4_21324.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_HS_i5006_DY330_rep4_21324.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep1_20223.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep1_20223.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep2_20224.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep2_20224.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep3_21316.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep3_21316.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep4_21317.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoC_MHS_i5006_DY330_rep4_21317.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_HS_i5006_DY330_rep1_17261.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_HS_i5006_DY330_rep1_17261.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_HS_i5006_DY330_rep2_17276.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_HS_i5006_DY330_rep2_17276.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_MHS_i5006_DY330_rep1_17253.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_MHS_i5006_DY330_rep1_17253.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_MHS_i5006_DY330_rep2_17269.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoD_MHS_i5006_DY330_rep2_17269.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep1_17265.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep1_17265.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep2_17280.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep2_17280.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep3_21313.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep3_21313.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep4_21314.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_HS_i5006_DY330_rep4_21314.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep1_17257.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep1_17257.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep2_17273.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep2_17273.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep3_21305.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep3_21305.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep4_21306.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoH_MHS_i5006_DY330_rep4_21306.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_HS_i5006_DY330_rep1_20229.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_HS_i5006_DY330_rep1_20229.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_HS_i5006_DY330_rep2_20230.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_HS_i5006_DY330_rep2_20230.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_MHS_i5006_DY330_rep1_20221.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_MHS_i5006_DY330_rep1_20221.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_MHS_i5006_DY330_rep2_20222.PE.a.bam --out 01-E.coli-MglB-Fis-HimD-Rpo_s-GSE189206/RpoN_MHS_i5006_DY330_rep2_20222.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoB_1.1x36mers.unique.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoB_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoB_1.SE.a.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoB_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoB_2.1x36mers.unique.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoB_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoB_2.SE.a.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoB_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoD_1.1x36mers.unique.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoD_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoD_1.SE.a.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoD_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoD_2.1x36mers.unique.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoD_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 02-E.coli-RpoB-RpoD-GSE182128/RpoD_2.SE.a.bam --out 02-E.coli-RpoB-RpoD-GSE182128/RpoD_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_DPD_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/Fur_with_Fe_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_DPD_and_rifampicin_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_1.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_1.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_2.1x36mers.unique.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_2.SE.a.bam --out 03-E.coli-Fur-RpoB-GSE54899/RpoB_with_Fe_and_rifampicin_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 04-E.coli-ArgR-GSE60546/ArgR_arg_rep1.1x36mers.unique.bam --out 04-E.coli-ArgR-GSE60546/ArgR_arg_rep1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 04-E.coli-ArgR-GSE60546/ArgR_arg_rep1.SE.a.bam --out 04-E.coli-ArgR-GSE60546/ArgR_arg_rep1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 04-E.coli-ArgR-GSE60546/ArgR_arg_rep2.1x36mers.unique.bam --out 04-E.coli-ArgR-GSE60546/ArgR_arg_rep2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 04-E.coli-ArgR-GSE60546/ArgR_arg_rep2.SE.a.bam --out 04-E.coli-ArgR-GSE60546/ArgR_arg_rep2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_1.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_1.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_2.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_2.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadE_pH5.5_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_1.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_1.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_2.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_2.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadW_pH5.5_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_1.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_1.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_2.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_2.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_GadX_pH5.5_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_1.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_1.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_2.1x36mers.unique.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_2.SE.a.bam --out 05-E.coli-GadEWX-GSE66441/ChIP-exo_RpoS_pH5.5_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 06-E.coli-UvrY-GSE74810/UvrY-ChIP-exo.1x36mers.unique.bam --out 06-E.coli-UvrY-GSE74810/UvrY-ChIP-exo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 06-E.coli-UvrY-GSE74810/UvrY-ChIP-exo.SE.a.bam --out 06-E.coli-UvrY-GSE74810/UvrY-ChIP-exo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod.1x36mers.unique.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod.SE.a.bam --out 07-E.coli-Crp-GSE64847/ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1-2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1-2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1-2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1-2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2-2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2-2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2-2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2-2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_no_rifampicin_applied_replicate_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_exponential_aerobic_growth_rifampicin_applied_for_20_minutes_replicate_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_1.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_1.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_2.1x36mers.unique.bam --out 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_2.SE.a.bam --out 08-E.coli-Sig70-GSE84830/Sig70_static_aerobic_growth_no_rifampicin_applied_replicate_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 09-E.coli-OmpR-GSE88979/OmpR_NaCl_1.1x36mers.unique.bam --out 09-E.coli-OmpR-GSE88979/OmpR_NaCl_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 09-E.coli-OmpR-GSE88979/OmpR_NaCl_1.SE.a.bam --out 09-E.coli-OmpR-GSE88979/OmpR_NaCl_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 09-E.coli-OmpR-GSE88979/OmpR_NaCl_2.1x36mers.unique.bam --out 09-E.coli-OmpR-GSE88979/OmpR_NaCl_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 09-E.coli-OmpR-GSE88979/OmpR_NaCl_2.SE.a.bam --out 09-E.coli-OmpR-GSE88979/OmpR_NaCl_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_acetate_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_fructose_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/Cra_glucose_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_cra_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_del_crp_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_1.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_1.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_2.1x36mers.unique.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_2.SE.a.bam --out 10-E.coli-Cra-RpoB-GSE65641/RpoB_WT_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc1_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc1_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/RpoB_glc2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc1_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc1_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YafC_glc2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc1_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc1_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaO_glc2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc1_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc1_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbaQ_glc2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbiH_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbiH_glc1_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbiH_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YbiH_glc1_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/Ybih_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/Ybih_glc2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/Ybih_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/Ybih_glc2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace1_ChIPexp.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace1_ChIPexp.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace1_ChIPexp.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace1_ChIPexp.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ace2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc1_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc1_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_glc2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_1_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_1_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph5_2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_1_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_1_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YdcI_ph8_2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc1_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc1_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YddM_glc2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc1_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc1_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YeiE_glc2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc1_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc1_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YheO_glc2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc1_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc1_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YiaJ_glc2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc1_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc1_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc1_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc1_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc2_ChIPexo.1x36mers.unique.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc2_ChIPexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc2_ChIPexo.SE.a.bam --out 11-E.coli-Yaf-Yba-Ybi-Ydd-Yhe-Yia-Yie-RpoB-GSE111095/YieP_glc2_ChIPexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 12-E.coli-cysB-metJ-GSE122320/cysB_taur_1_ChIPexo.PE.a.bam --out 12-E.coli-cysB-metJ-GSE122320/cysB_taur_1_ChIPexo.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 12-E.coli-cysB-metJ-GSE122320/cysB_taur_2_ChIPexo.PE.a.bam --out 12-E.coli-cysB-metJ-GSE122320/cysB_taur_2_ChIPexo.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 12-E.coli-cysB-metJ-GSE122320/metJ_meio_1_ChIPexo.PE.a.bam --out 12-E.coli-cysB-metJ-GSE122320/metJ_meio_1_ChIPexo.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 12-E.coli-cysB-metJ-GSE122320/metJ_meio_2_ChIPexo.PE.a.bam --out 12-E.coli-cysB-metJ-GSE122320/metJ_meio_2_ChIPexo.PE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep1.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep1.SE.a.bam --out 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep2.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep2.SE.a.bam --out 13-E.coli-SigH-GSE60667/RNAP_beta_42C_rep2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_30C_rep1.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/SigH_30C_rep1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_30C_rep1.SE.a.bam --out 13-E.coli-SigH-GSE60667/SigH_30C_rep1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_30C_rep2.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/SigH_30C_rep2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_30C_rep2.SE.a.bam --out 13-E.coli-SigH-GSE60667/SigH_30C_rep2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_42C_rep1.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/SigH_42C_rep1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_42C_rep1.SE.a.bam --out 13-E.coli-SigH-GSE60667/SigH_42C_rep1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_42C_rep2.1x36mers.unique.bam --out 13-E.coli-SigH-GSE60667/SigH_42C_rep2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 13-E.coli-SigH-GSE60667/SigH_42C_rep2.SE.a.bam --out 13-E.coli-SigH-GSE60667/SigH_42C_rep2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_1.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_1.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_2.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_2.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yahB_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_1.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_1.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_2.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_2.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yiaU_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_1.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_1.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_2.1x36mers.unique.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_2.SE.a.bam --out 14-E.coli-YqhC-YiaU-YahB-GSE158683/yqhC_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR1_Chipexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR1_Chipexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR2_Chipexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/BaeR2_Chipexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR1_Chipexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR1_Chipexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR2_Chipexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/CpxR2_Chipexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE1_Chipexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE1_Chipexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE2_Chipexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/KdpE2_Chipexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB1_Chipexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB1_Chipexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB2_Chipexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/PhoB2_Chipexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR1_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR1_Chipexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR1_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR1_Chipexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR2_Chipexo.1x36mers.unique.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR2_Chipexo.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR2_Chipexo.SE.a.bam --out 15-E.coli-BaeSR-CpxAR-KdpDE-PhoRB-ZraSR-GSE143851/ZraR2_Chipexo.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 16-E.coli-ydhB-GSE166465/ydhB_1.1x36mers.unique.bam --out 16-E.coli-ydhB-GSE166465/ydhB_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 16-E.coli-ydhB-GSE166465/ydhB_1.SE.a.bam --out 16-E.coli-ydhB-GSE166465/ydhB_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 16-E.coli-ydhB-GSE166465/ydhB_2.1x36mers.unique.bam --out 16-E.coli-ydhB-GSE166465/ydhB_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 16-E.coli-ydhB-GSE166465/ydhB_2.SE.a.bam --out 16-E.coli-ydhB-GSE166465/ydhB_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Dps_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Fis_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrA_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/GyrB_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/H-NS_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupA_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/HupB_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/InfA_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/MukB_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/RdgC_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Rob_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/StpA_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/TopA_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_1.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_1.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_2.1x36mers.unique.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_2.SE.a.bam --out 17-E.coli-nucleoid_associated_proteins-GSE181767/Tus_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/narL_1.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/narL_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/narL_1.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/narL_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/narL_2.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/narL_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/narL_2.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/narL_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_1.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_1.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_2.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_2.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/puuR_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_1.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_1.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_2.1x36mers.unique.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_2.SE.a.bam --out 18-E.coli-narL-puuR-rcsA-GSE181772/rcsA_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 19-E.coli-ZraR-GSE181993/ZraR_1.1x36mers.unique.bam --out 19-E.coli-ZraR-GSE181993/ZraR_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 19-E.coli-ZraR-GSE181993/ZraR_1.SE.a.bam --out 19-E.coli-ZraR-GSE181993/ZraR_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 19-E.coli-ZraR-GSE181993/ZraR_2.1x36mers.unique.bam --out 19-E.coli-ZraR-GSE181993/ZraR_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 19-E.coli-ZraR-GSE181993/ZraR_2.SE.a.bam --out 19-E.coli-ZraR-GSE181993/ZraR_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/rpoB_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/rpoD_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yahB_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybcM_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybdO_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybeF_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ybhD_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycaN_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycfQ_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yciT_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ycjW_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydcN_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydcR_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydhB_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ydiP_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yeaM_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yebK_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yedW_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yeeY_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yehT_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfeC_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfeD_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfiE_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yfjR_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygaV_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygbI_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygeR_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ygfI_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yggD_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yhjB_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yhjC_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yiaU_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yidL_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yidZ_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yihL_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yihW_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yjhI_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yneJ_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ynfL_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/ypdC_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_1.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_1.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_2.1x36mers.unique.bam --out 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_2.SE.a.bam --out 20-E.coli-uncharacterized-GSE159777/yqhC_myc-tag_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_1.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_1.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2A1.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2A1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2A1.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2A1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2B6.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2B6.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2B6.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2B6.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2C4.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2C4.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2C4.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2C4.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2D6.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2D6.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2D6.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2D6.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_2.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4A1.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4A1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4A1.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4A1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4A3.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4A3.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4A3.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4A3.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4D6.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4D6.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_4D6.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_4D6.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5A10.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5A10.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5A10.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5A10.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5B6.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5B6.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5B6.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5B6.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5B9.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5B9.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5B9.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5B9.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5F9.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5F9.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5F9.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5F9.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5G8.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5G8.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_5G8.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_5G8.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_7B10.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_7B10.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_7B10.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_7B10.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_8B2.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_8B2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_8B2.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_8B2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_M2.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_M2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_M2.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_M2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_M4.1x36mers.unique.bam --out 21-E.coli-ArcA-GSE182077/ArcA_M4.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 21-E.coli-ArcA-GSE182077/ArcA_M4.SE.a.bam --out 21-E.coli-ArcA-GSE182077/ArcA_M4.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_ammonia_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytidine_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_cytosine_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/Nac_glutamine_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_ammonia_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytidine_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_cytosine_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/NtrC_glutamine_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_ammonia_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytidine_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_cytosine_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoD_glutamine_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_ammonia_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytidine_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_cytosine_2.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_1.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_1.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_1.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_1.SE.a.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_2.1x36mers.unique.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_2.1x36mers.unique.GPS
java -Xmx10G -jar /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/gem.jar --min 10 --f SAM --d /oak/stanford/groups/akundaje/marinovg/programs/gem.v3.2/Read_Distribution_ChIP-exo.txt --expt 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_2.SE.a.bam --out 22-E.coli-NtrC-Nac-GSE54902/RpoN_glutamine_2.SE.a.GPS