cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=HA-RpaA_culture_anti-HA_peak_binding_ZT_36h-GSM1238668.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=HA-RpaA_culture_anti-HA_peak_binding_ZT_36h-GSM1238668.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_anti-HA_peak_binding_ZT_32h-GSM1238669.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_anti-HA_peak_binding_ZT_32h-GSM1238669.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_anti-RpaA_ZT_24h_Rep1-GSM1238657.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_anti-RpaA_ZT_24h_Rep1-GSM1238657.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_anti-RpaA_ZT_28h_Rep1-GSM1238658.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_anti-RpaA_ZT_28h_Rep1-GSM1238658.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_anti-RpaA_ZT_32h_Rep1-GSM1238659.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_anti-RpaA_ZT_32h_Rep1-GSM1238659.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_anti-RpaA_ZT_36h_Rep1-GSM1238660.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_anti-RpaA_ZT_36h_Rep1-GSM1238660.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_anti-RpaA_ZT_40h_Rep1-GSM1238661.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_anti-RpaA_ZT_40h_Rep1-GSM1238661.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_anti-RpaA_ZT_44h_Rep1-GSM1238662.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_anti-RpaA_ZT_44h_Rep1-GSM1238662.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_anti-RpaA_ZT_48h_Rep1-GSM1238663.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_anti-RpaA_ZT_48h_Rep1-GSM1238663.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_anti-RpaA_peak_binding_ZT_32h_Rep2-GSM1238666.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_anti-RpaA_peak_binding_ZT_32h_Rep2-GSM1238666.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_anti-RpaA_trough_binding_ZT_44h_Rep2-GSM1238667.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_anti-RpaA_trough_binding_ZT_44h_Rep2-GSM1238667.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_input_DNA_at_peak_binding_ZT_32h_Rep1-GSM1238670.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_input_DNA_at_peak_binding_ZT_32h_Rep1-GSM1238670.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_input_DNA_at_peak_binding_ZT_32h_Rep2-GSM1238672.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_input_DNA_at_peak_binding_ZT_32h_Rep2-GSM1238672.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_input_DNA_at_peak_binding_ZT_44h_Rep1-GSM1238671.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_input_DNA_at_peak_binding_ZT_44h_Rep1-GSM1238671.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=WT_culture_input_DNA_at_peak_binding_ZT_44h_Rep2-GSM1238673.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=WT_culture_input_DNA_at_peak_binding_ZT_44h_Rep2-GSM1238673.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=delrpaA_culture_anti-RpaA_pool_of_ZT_24-44h_Rep1-GSM1238664.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=delrpaA_culture_anti-RpaA_pool_of_ZT_24-44h_Rep1-GSM1238664.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=delrpaA_culture_anti-RpaA_pool_of_ZT_24-44h_Rep2-GSM1238665.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=delrpaA_culture_anti-RpaA_pool_of_ZT_24-44h_Rep2-GSM1238665.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=delrpaA_culture_input_DNA_for_ZT_24-44h_pool_Rep1-GSM1238674.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=delrpaA_culture_input_DNA_for_ZT_24-44h_pool_Rep1-GSM1238674.32mers.unique.QC
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/10-Synechococcus_elongatus_PCC_7942; module load openmpi; Rscript /N/dc2/projects/marinovg/code/spp/spp_package/run_spp.R -c=delrpaA_culture_input_DNA_for_ZT_24-44h_pool_Rep2-GSM1238675.32mers.unique.bam -p=16 -savp -rf -s=-0:2:400 -out=delrpaA_culture_input_DNA_for_ZT_24-44h_pool_Rep2-GSM1238675.32mers.unique.QC