Command line arguments

-type histone -final_stage idr -out_dir /projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/Microglia -title Microglia -species hg19 -nth 1 -no_jsd -tag1 /projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/10288185/Microglia/align/pooled_rep/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.tagAlign.gz -tag2 /projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/10514454/Microglia/align/pooled_rep/H3K27ac_PU.1+_4454_hpc_1.nodup_H3K27ac_PU.1+_4454_hpc_2.nodup.tagAlign.gz -tag3 /projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/11409232/Microglia/align/pooled_rep/H3K27ac_PU.1+_9232_hpc_1.nodup_H3K27ac_PU.1+_9232_hpc_2.nodup.tagAlign.gz -tag4 /projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/20104101/Microglia/align/pooled_rep/H3K27ac_PU.1+_4101_hpc_1.nodup_H3K27ac_PU.1+_4101_hpc_2.nodup.tagAlign.gz -tag5 /projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/21142003/Microglia/align/pooled_rep/H3K27ac_PU.1+_2003_hpc_1.nodup_H3K27ac_PU.1+_2003_hpc_2.nodup.tagAlign.gz -tag6 /projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/21412626/Microglia/align/pooled_rep/H3K27ac_PU.1+_2626_hpc_1.nodup_H3K27ac_PU.1+_2626_hpc_2.nodup.tagAlign.gz -ctl_tag1 /projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/10288185/Microglia/align/pooled_ctl/Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup.tagAlign.gz -ctl_tag2 /projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/10514454/Microglia/align/pooled_ctl/Input_PU.1+_4454_hpc_1.nodup_Input_PU.1+_4454_hpc_2.nodup.tagAlign.gz -ctl_tag3 /projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/11409232/Microglia/align/pooled_ctl/Input_PU.1+_9232_hpc_1.nodup_Input_PU.1+_9232_hpc_2.nodup.tagAlign.gz -ctl_tag4 /projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/20104101/Microglia/align/pooled_ctl/Input_PU.1+_4101_hpc_1.nodup_Input_PU.1+_4101_hpc_2.nodup.tagAlign.gz -ctl_tag5 /projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/21142003/Microglia/align/pooled_ctl/Input_PU.1+_2003_hpc_1.nodup_Input_PU.1+_2003_hpc_2.nodup.tagAlign.gz -ctl_tag6 /projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/21412626/Microglia/align/pooled_ctl/Input_PU.1+_2626_hpc_1.nodup_Input_PU.1+_2626_hpc_2.nodup.tagAlign.gz

Directories and files

Expand all Collapse all
Files	Path
Alignment
Replicate 1
Tag-align	/projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/10288185/Microglia/align/pooled_rep/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.tagAlign.gz
Replicate 2
Tag-align	/projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/10514454/Microglia/align/pooled_rep/H3K27ac_PU.1+_4454_hpc_1.nodup_H3K27ac_PU.1+_4454_hpc_2.nodup.tagAlign.gz
Replicate 3
Tag-align	/projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/11409232/Microglia/align/pooled_rep/H3K27ac_PU.1+_9232_hpc_1.nodup_H3K27ac_PU.1+_9232_hpc_2.nodup.tagAlign.gz
Replicate 4
Tag-align	/projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/20104101/Microglia/align/pooled_rep/H3K27ac_PU.1+_4101_hpc_1.nodup_H3K27ac_PU.1+_4101_hpc_2.nodup.tagAlign.gz
Replicate 5
Tag-align	/projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/21142003/Microglia/align/pooled_rep/H3K27ac_PU.1+_2003_hpc_1.nodup_H3K27ac_PU.1+_2003_hpc_2.nodup.tagAlign.gz
Replicate 6
Tag-align	/projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/21412626/Microglia/align/pooled_rep/H3K27ac_PU.1+_2626_hpc_1.nodup_H3K27ac_PU.1+_2626_hpc_2.nodup.tagAlign.gz
Control 1
Tag-align	/projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/10288185/Microglia/align/pooled_ctl/Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup.tagAlign.gz
Control 2
Tag-align	/projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/10514454/Microglia/align/pooled_ctl/Input_PU.1+_4454_hpc_1.nodup_Input_PU.1+_4454_hpc_2.nodup.tagAlign.gz
Control 3
Tag-align	/projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/11409232/Microglia/align/pooled_ctl/Input_PU.1+_9232_hpc_1.nodup_Input_PU.1+_9232_hpc_2.nodup.tagAlign.gz
Control 4
Tag-align	/projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/20104101/Microglia/align/pooled_ctl/Input_PU.1+_4101_hpc_1.nodup_Input_PU.1+_4101_hpc_2.nodup.tagAlign.gz
Control 5
Tag-align	/projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/21142003/Microglia/align/pooled_ctl/Input_PU.1+_2003_hpc_1.nodup_Input_PU.1+_2003_hpc_2.nodup.tagAlign.gz
Control 6
Tag-align	/projects/pfenninggroup/jemmie/gwyn_hpc_3exphg/peaks/controls/21412626/Microglia/align/pooled_ctl/Input_PU.1+_2626_hpc_1.nodup_Input_PU.1+_2626_hpc_2.nodup.tagAlign.gz
Pooled replicate
Tag-align	./align/pooled_rep/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.gz
Pooled control
Tag-align	./align/pooled_ctl/Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Tag-align	./align/pseudo_reps/rep1/pr1/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align	./align/pseudo_reps/rep1/pr2/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.pr2.tagAlign.gz
Replicate 2
Pseudo-replicate 1
Tag-align	./align/pseudo_reps/rep2/pr1/H3K27ac_PU.1+_4454_hpc_1.nodup_H3K27ac_PU.1+_4454_hpc_2.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align	./align/pseudo_reps/rep2/pr2/H3K27ac_PU.1+_4454_hpc_1.nodup_H3K27ac_PU.1+_4454_hpc_2.nodup.pr2.tagAlign.gz
Replicate 3
Pseudo-replicate 1
Tag-align	./align/pseudo_reps/rep3/pr1/H3K27ac_PU.1+_9232_hpc_1.nodup_H3K27ac_PU.1+_9232_hpc_2.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align	./align/pseudo_reps/rep3/pr2/H3K27ac_PU.1+_9232_hpc_1.nodup_H3K27ac_PU.1+_9232_hpc_2.nodup.pr2.tagAlign.gz
Replicate 4
Pseudo-replicate 1
Tag-align	./align/pseudo_reps/rep4/pr1/H3K27ac_PU.1+_4101_hpc_1.nodup_H3K27ac_PU.1+_4101_hpc_2.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align	./align/pseudo_reps/rep4/pr2/H3K27ac_PU.1+_4101_hpc_1.nodup_H3K27ac_PU.1+_4101_hpc_2.nodup.pr2.tagAlign.gz
Replicate 5
Pseudo-replicate 1
Tag-align	./align/pseudo_reps/rep5/pr1/H3K27ac_PU.1+_2003_hpc_1.nodup_H3K27ac_PU.1+_2003_hpc_2.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align	./align/pseudo_reps/rep5/pr2/H3K27ac_PU.1+_2003_hpc_1.nodup_H3K27ac_PU.1+_2003_hpc_2.nodup.pr2.tagAlign.gz
Replicate 6
Pseudo-replicate 1
Tag-align	./align/pseudo_reps/rep6/pr1/H3K27ac_PU.1+_2626_hpc_1.nodup_H3K27ac_PU.1+_2626_hpc_2.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align	./align/pseudo_reps/rep6/pr2/H3K27ac_PU.1+_2626_hpc_1.nodup_H3K27ac_PU.1+_2626_hpc_2.nodup.pr2.tagAlign.gz
Pooled pseudo-replicates
Pooled pseudo-replicate 1
Tag-align	./align/pooled_pseudo_reps/ppr1/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.pr1_pooled.tagAlign.gz
Pooled pseudo-replicate 2
Tag-align	./align/pooled_pseudo_reps/ppr2/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.pr2_pooled.tagAlign.gz
Signal tracks
MACS2
Replicate 1
P-value	./signal/macs2/rep1/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval.signal.bw
Fold enrichment	./signal/macs2/rep1/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.fc.signal.bw
Replicate 2
P-value	./signal/macs2/rep2/H3K27ac_PU.1+_4454_hpc_1.nodup_H3K27ac_PU.1+_4454_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval.signal.bw
Fold enrichment	./signal/macs2/rep2/H3K27ac_PU.1+_4454_hpc_1.nodup_H3K27ac_PU.1+_4454_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.fc.signal.bw
Replicate 3
P-value	./signal/macs2/rep3/H3K27ac_PU.1+_9232_hpc_1.nodup_H3K27ac_PU.1+_9232_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval.signal.bw
Fold enrichment	./signal/macs2/rep3/H3K27ac_PU.1+_9232_hpc_1.nodup_H3K27ac_PU.1+_9232_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.fc.signal.bw
Replicate 4
P-value	./signal/macs2/rep4/H3K27ac_PU.1+_4101_hpc_1.nodup_H3K27ac_PU.1+_4101_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval.signal.bw
Fold enrichment	./signal/macs2/rep4/H3K27ac_PU.1+_4101_hpc_1.nodup_H3K27ac_PU.1+_4101_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.fc.signal.bw
Replicate 5
P-value	./signal/macs2/rep5/H3K27ac_PU.1+_2003_hpc_1.nodup_H3K27ac_PU.1+_2003_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval.signal.bw
Fold enrichment	./signal/macs2/rep5/H3K27ac_PU.1+_2003_hpc_1.nodup_H3K27ac_PU.1+_2003_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.fc.signal.bw
Replicate 6
P-value	./signal/macs2/rep6/H3K27ac_PU.1+_2626_hpc_1.nodup_H3K27ac_PU.1+_2626_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval.signal.bw
Fold enrichment	./signal/macs2/rep6/H3K27ac_PU.1+_2626_hpc_1.nodup_H3K27ac_PU.1+_2626_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.fc.signal.bw
Pooled replicate
P-value	./signal/macs2/pooled_rep/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup_pooled.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval.signal.bw
Fold enrichment	./signal/macs2/pooled_rep/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup_pooled.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.fc.signal.bw
Peaks
MACS2
Replicate 1
Narrow peak	./peak/macs2/rep1/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Replicate 2
Narrow peak	./peak/macs2/rep2/H3K27ac_PU.1+_4454_hpc_1.nodup_H3K27ac_PU.1+_4454_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Replicate 3
Narrow peak	./peak/macs2/rep3/H3K27ac_PU.1+_9232_hpc_1.nodup_H3K27ac_PU.1+_9232_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Replicate 4
Narrow peak	./peak/macs2/rep4/H3K27ac_PU.1+_4101_hpc_1.nodup_H3K27ac_PU.1+_4101_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Replicate 5
Narrow peak	./peak/macs2/rep5/H3K27ac_PU.1+_2003_hpc_1.nodup_H3K27ac_PU.1+_2003_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Replicate 6
Narrow peak	./peak/macs2/rep6/H3K27ac_PU.1+_2626_hpc_1.nodup_H3K27ac_PU.1+_2626_hpc_2.nodup.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Pooled replicate
Narrow peak	./peak/macs2/pooled_rep/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup_pooled.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Narrow peak	./peak/macs2/pseudo_reps/rep1/pr1/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.pr1.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Pseudo-replicate 2
Narrow peak	./peak/macs2/pseudo_reps/rep1/pr2/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.pr2.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Replicate 2
Pseudo-replicate 1
Narrow peak	./peak/macs2/pseudo_reps/rep2/pr1/H3K27ac_PU.1+_4454_hpc_1.nodup_H3K27ac_PU.1+_4454_hpc_2.nodup.pr1.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Pseudo-replicate 2
Narrow peak	./peak/macs2/pseudo_reps/rep2/pr2/H3K27ac_PU.1+_4454_hpc_1.nodup_H3K27ac_PU.1+_4454_hpc_2.nodup.pr2.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Replicate 3
Pseudo-replicate 1
Narrow peak	./peak/macs2/pseudo_reps/rep3/pr1/H3K27ac_PU.1+_9232_hpc_1.nodup_H3K27ac_PU.1+_9232_hpc_2.nodup.pr1.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Pseudo-replicate 2
Narrow peak	./peak/macs2/pseudo_reps/rep3/pr2/H3K27ac_PU.1+_9232_hpc_1.nodup_H3K27ac_PU.1+_9232_hpc_2.nodup.pr2.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Replicate 4
Pseudo-replicate 1
Narrow peak	./peak/macs2/pseudo_reps/rep4/pr1/H3K27ac_PU.1+_4101_hpc_1.nodup_H3K27ac_PU.1+_4101_hpc_2.nodup.pr1.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Pseudo-replicate 2
Narrow peak	./peak/macs2/pseudo_reps/rep4/pr2/H3K27ac_PU.1+_4101_hpc_1.nodup_H3K27ac_PU.1+_4101_hpc_2.nodup.pr2.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Replicate 5
Pseudo-replicate 1
Narrow peak	./peak/macs2/pseudo_reps/rep5/pr1/H3K27ac_PU.1+_2003_hpc_1.nodup_H3K27ac_PU.1+_2003_hpc_2.nodup.pr1.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Pseudo-replicate 2
Narrow peak	./peak/macs2/pseudo_reps/rep5/pr2/H3K27ac_PU.1+_2003_hpc_1.nodup_H3K27ac_PU.1+_2003_hpc_2.nodup.pr2.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Replicate 6
Pseudo-replicate 1
Narrow peak	./peak/macs2/pseudo_reps/rep6/pr1/H3K27ac_PU.1+_2626_hpc_1.nodup_H3K27ac_PU.1+_2626_hpc_2.nodup.pr1.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Pseudo-replicate 2
Narrow peak	./peak/macs2/pseudo_reps/rep6/pr2/H3K27ac_PU.1+_2626_hpc_1.nodup_H3K27ac_PU.1+_2626_hpc_2.nodup.pr2.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Pooled pseudo-replicate
Pooled pseudo-replicate 1
Narrow peak	./peak/macs2/pooled_pseudo_reps/ppr1/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.pr1_pooled.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Pooled pseudo-replicate 2
Narrow peak	./peak/macs2/pooled_pseudo_reps/ppr2/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.pr2_pooled.tagAlign_x_Input_PU.1+_8185_hpc_1.nodup_Input_PU.1+_8185_hpc_2.nodup_pooled.tagAlign.pval0.01.500K.narrowPeak.gz
Naive overlap
True replicates
Rep. 1 vs. Rep. 2
Overlapping peak	./peak/macs2/overlap/true_reps/rep1-rep2/Microglia_rep1-rep2.naive_overlap.filt.narrowPeak.gz
Rep. 1 vs. Rep. 3
Overlapping peak	./peak/macs2/overlap/true_reps/rep1-rep3/Microglia_rep1-rep3.naive_overlap.filt.narrowPeak.gz
Rep. 1 vs. Rep. 4
Overlapping peak	./peak/macs2/overlap/true_reps/rep1-rep4/Microglia_rep1-rep4.naive_overlap.filt.narrowPeak.gz
Rep. 1 vs. Rep. 5
Overlapping peak	./peak/macs2/overlap/true_reps/rep1-rep5/Microglia_rep1-rep5.naive_overlap.filt.narrowPeak.gz
Rep. 1 vs. Rep. 6
Overlapping peak	./peak/macs2/overlap/true_reps/rep1-rep6/Microglia_rep1-rep6.naive_overlap.filt.narrowPeak.gz
Rep. 2 vs. Rep. 3
Overlapping peak	./peak/macs2/overlap/true_reps/rep2-rep3/Microglia_rep2-rep3.naive_overlap.filt.narrowPeak.gz
Rep. 2 vs. Rep. 4
Overlapping peak	./peak/macs2/overlap/true_reps/rep2-rep4/Microglia_rep2-rep4.naive_overlap.filt.narrowPeak.gz
Rep. 2 vs. Rep. 5
Overlapping peak	./peak/macs2/overlap/true_reps/rep2-rep5/Microglia_rep2-rep5.naive_overlap.filt.narrowPeak.gz
Rep. 2 vs. Rep. 6
Overlapping peak	./peak/macs2/overlap/true_reps/rep2-rep6/Microglia_rep2-rep6.naive_overlap.filt.narrowPeak.gz
Rep. 3 vs. Rep. 4
Overlapping peak	./peak/macs2/overlap/true_reps/rep3-rep4/Microglia_rep3-rep4.naive_overlap.filt.narrowPeak.gz
Rep. 3 vs. Rep. 5
Overlapping peak	./peak/macs2/overlap/true_reps/rep3-rep5/Microglia_rep3-rep5.naive_overlap.filt.narrowPeak.gz
Rep. 3 vs. Rep. 6
Overlapping peak	./peak/macs2/overlap/true_reps/rep3-rep6/Microglia_rep3-rep6.naive_overlap.filt.narrowPeak.gz
Rep. 4 vs. Rep. 5
Overlapping peak	./peak/macs2/overlap/true_reps/rep4-rep5/Microglia_rep4-rep5.naive_overlap.filt.narrowPeak.gz
Rep. 4 vs. Rep. 6
Overlapping peak	./peak/macs2/overlap/true_reps/rep4-rep6/Microglia_rep4-rep6.naive_overlap.filt.narrowPeak.gz
Rep. 5 vs. Rep. 6
Overlapping peak	./peak/macs2/overlap/true_reps/rep5-rep6/Microglia_rep5-rep6.naive_overlap.filt.narrowPeak.gz
Pseudo-replicates
Replicate 1
Overlapping peak	./peak/macs2/overlap/pseudo_reps/rep1/Microglia_rep1-pr.naive_overlap.filt.narrowPeak.gz
Replicate 2
Overlapping peak	./peak/macs2/overlap/pseudo_reps/rep2/Microglia_rep2-pr.naive_overlap.filt.narrowPeak.gz
Replicate 3
Overlapping peak	./peak/macs2/overlap/pseudo_reps/rep3/Microglia_rep3-pr.naive_overlap.filt.narrowPeak.gz
Replicate 4
Overlapping peak	./peak/macs2/overlap/pseudo_reps/rep4/Microglia_rep4-pr.naive_overlap.filt.narrowPeak.gz
Replicate 5
Overlapping peak	./peak/macs2/overlap/pseudo_reps/rep5/Microglia_rep5-pr.naive_overlap.filt.narrowPeak.gz
Replicate 6
Overlapping peak	./peak/macs2/overlap/pseudo_reps/rep6/Microglia_rep6-pr.naive_overlap.filt.narrowPeak.gz
Pooled pseudo-replicates
Overlapping peak	./peak/macs2/overlap/pooled_pseudo_reps/Microglia_ppr.naive_overlap.filt.narrowPeak.gz
Optimal set
Overlapping peak	./peak/macs2/overlap/optimal_set/Microglia_ppr.naive_overlap.filt.narrowPeak.gz
Conservative set
Overlapping peak	./peak/macs2/overlap/conservative_set/Microglia_rep4-rep6.naive_overlap.filt.narrowPeak.gz
QC and logs
Replicate 1
Cross-corr. log	./qc/rep1/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.no_chrM.15M.cc.qc
Cross-corr. plot	./qc/rep1/H3K27ac_PU.1+_8185_hpc_1.nodup_H3K27ac_PU.1+_8185_hpc_2.nodup.no_chrM.15M.cc.plot.pdf
Replicate 2
Cross-corr. log	./qc/rep2/H3K27ac_PU.1+_4454_hpc_1.nodup_H3K27ac_PU.1+_4454_hpc_2.nodup.no_chrM.15M.cc.qc
Cross-corr. plot	./qc/rep2/H3K27ac_PU.1+_4454_hpc_1.nodup_H3K27ac_PU.1+_4454_hpc_2.nodup.no_chrM.15M.cc.plot.pdf
Replicate 3
Cross-corr. log	./qc/rep3/H3K27ac_PU.1+_9232_hpc_1.nodup_H3K27ac_PU.1+_9232_hpc_2.nodup.no_chrM.15M.cc.qc
Cross-corr. plot	./qc/rep3/H3K27ac_PU.1+_9232_hpc_1.nodup_H3K27ac_PU.1+_9232_hpc_2.nodup.no_chrM.15M.cc.plot.pdf
Replicate 4
Cross-corr. log	./qc/rep4/H3K27ac_PU.1+_4101_hpc_1.nodup_H3K27ac_PU.1+_4101_hpc_2.nodup.no_chrM.15M.cc.qc
Cross-corr. plot	./qc/rep4/H3K27ac_PU.1+_4101_hpc_1.nodup_H3K27ac_PU.1+_4101_hpc_2.nodup.no_chrM.15M.cc.plot.pdf
Replicate 5
Cross-corr. log	./qc/rep5/H3K27ac_PU.1+_2003_hpc_1.nodup_H3K27ac_PU.1+_2003_hpc_2.nodup.no_chrM.15M.cc.qc
Cross-corr. plot	./qc/rep5/H3K27ac_PU.1+_2003_hpc_1.nodup_H3K27ac_PU.1+_2003_hpc_2.nodup.no_chrM.15M.cc.plot.pdf
Replicate 6
Cross-corr. log	./qc/rep6/H3K27ac_PU.1+_2626_hpc_1.nodup_H3K27ac_PU.1+_2626_hpc_2.nodup.no_chrM.15M.cc.qc
Cross-corr. plot	./qc/rep6/H3K27ac_PU.1+_2626_hpc_1.nodup_H3K27ac_PU.1+_2626_hpc_2.nodup.no_chrM.15M.cc.plot.pdf
Naive overlap
Overlap QC log	./qc/Microglia_peak_overlap_final.qc
True replicates
Rep. 1 vs. Rep. 2
FRiP	./peak/macs2/overlap/true_reps/rep1-rep2/Microglia_rep1-rep2.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 1 vs. Rep. 3
FRiP	./peak/macs2/overlap/true_reps/rep1-rep3/Microglia_rep1-rep3.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 1 vs. Rep. 4
FRiP	./peak/macs2/overlap/true_reps/rep1-rep4/Microglia_rep1-rep4.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 1 vs. Rep. 5
FRiP	./peak/macs2/overlap/true_reps/rep1-rep5/Microglia_rep1-rep5.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 1 vs. Rep. 6
FRiP	./peak/macs2/overlap/true_reps/rep1-rep6/Microglia_rep1-rep6.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 2 vs. Rep. 3
FRiP	./peak/macs2/overlap/true_reps/rep2-rep3/Microglia_rep2-rep3.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 2 vs. Rep. 4
FRiP	./peak/macs2/overlap/true_reps/rep2-rep4/Microglia_rep2-rep4.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 2 vs. Rep. 5
FRiP	./peak/macs2/overlap/true_reps/rep2-rep5/Microglia_rep2-rep5.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 2 vs. Rep. 6
FRiP	./peak/macs2/overlap/true_reps/rep2-rep6/Microglia_rep2-rep6.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 3 vs. Rep. 4
FRiP	./peak/macs2/overlap/true_reps/rep3-rep4/Microglia_rep3-rep4.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 3 vs. Rep. 5
FRiP	./peak/macs2/overlap/true_reps/rep3-rep5/Microglia_rep3-rep5.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 3 vs. Rep. 6
FRiP	./peak/macs2/overlap/true_reps/rep3-rep6/Microglia_rep3-rep6.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 4 vs. Rep. 5
FRiP	./peak/macs2/overlap/true_reps/rep4-rep5/Microglia_rep4-rep5.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 4 vs. Rep. 6
FRiP	./peak/macs2/overlap/true_reps/rep4-rep6/Microglia_rep4-rep6.naive_overlap.filt.narrowPeak.FRiP.qc
Rep. 5 vs. Rep. 6
FRiP	./peak/macs2/overlap/true_reps/rep5-rep6/Microglia_rep5-rep6.naive_overlap.filt.narrowPeak.FRiP.qc
Pseudo-replicates
Replicate 1
FRiP	./peak/macs2/overlap/pseudo_reps/rep1/Microglia_rep1-pr.naive_overlap.filt.narrowPeak.FRiP.qc
Replicate 2
FRiP	./peak/macs2/overlap/pseudo_reps/rep2/Microglia_rep2-pr.naive_overlap.filt.narrowPeak.FRiP.qc
Replicate 3
FRiP	./peak/macs2/overlap/pseudo_reps/rep3/Microglia_rep3-pr.naive_overlap.filt.narrowPeak.FRiP.qc
Replicate 4
FRiP	./peak/macs2/overlap/pseudo_reps/rep4/Microglia_rep4-pr.naive_overlap.filt.narrowPeak.FRiP.qc
Replicate 5
FRiP	./peak/macs2/overlap/pseudo_reps/rep5/Microglia_rep5-pr.naive_overlap.filt.narrowPeak.FRiP.qc
Replicate 6
FRiP	./peak/macs2/overlap/pseudo_reps/rep6/Microglia_rep6-pr.naive_overlap.filt.narrowPeak.FRiP.qc

Enrichment QC (strand cross-correlation measures)

	rep1	rep2	rep3	rep4	rep5	rep6
Reads	15000000	15000000	15000000	15000000	15000000	15000000
Est. Fragment Len.	195	205	185	195	200	210
Corr. Est. Fragment Len.	0.20892350928735	0.18434306397735	0.189194172908755	0.213012197829018	0.191337824770722	0.20898520699019
Phantom Peak	40	50	40	50	40	40
Corr. Phantom Peak	0.2064893	0.1845664	0.1899307	0.2104474	0.1913872	0.2072274
Argmin. Corr.	1500	1500	1500	1500	1500	1500
Min. Corr.	0.1889893	0.1800024	0.1830788	0.1921797	0.1825919	0.1902599
NSC	1.105478	1.024114	1.033403	1.108401	1.047899	1.09842
RSC	1.139095	0.9510615	0.8925114	1.140401	0.9943842	1.103599

NOTE: Reads from replicates are subsampled to a max of 15M

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Number of peaks

rep1	201991
rep1-pr1	175499
rep1-pr2	175531
rep2	220560
rep2-pr1	185107
rep2-pr2	185732
rep3	232520
rep3-pr1	216883
rep3-pr2	217163
rep4	193733
rep4-pr1	186294
rep4-pr2	186370
rep5	229830
rep5-pr1	194061
rep5-pr2	193792
rep6	176802
rep6-pr1	171242
rep6-pr2	170462
pooled	243780
ppr1	245190
ppr2	244426

ppr1: Raw peaks called on the first pooled pseudoreplicates
ppr2: Raw peaks called on the second pooled pseudoreplicates
repi: Raw peaks called on true replicate i
repi-pr1 : Raw peaks called on the first pseudoreplicate from replicate i
repi-pr2 : Raw peaks called on the second pseudoreplicates from replicate i
overlap : Overlapped peaks (filtered if blacklist exists)

Enrichment QC (Fraction of reads in raw peaks)

	pooled_rep	rep1	rep2	rep3	rep4	rep5	rep6
Fraction of Reads in Peak	0.408324	0.360662	0.228248	0.271706	0.396874	0.318603	0.387297

Enrichment QC (Fraction of reads in overlapping peaks)

	rep1-pr	rep1-rep2	rep1-rep3	rep1-rep4	rep1-rep5	rep1-rep6	rep2-pr	rep2-rep3	rep2-rep4	rep2-rep5	rep2-rep6	rep3-pr	rep3-rep4	rep3-rep5	rep3-rep6	rep4-pr	rep4-rep5	rep4-rep6	rep5-pr	rep5-rep6	rep6-pr
Fraction of Reads in Peak	0.301096	0.328671	0.334415	0.34081	0.339609	0.335431	0.14832	0.324196	0.32837	0.333128	0.321897	0.197343	0.336821	0.333531	0.332938	0.349011	0.339815	0.34001	0.255373	0.331538	0.3421

ppr: Overlapping peaks comparing pooled pseudo replicates
rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)

Reproducibility QC and Peak Detection Statistics (Overlapping peaks)

Nt	85158
N1	80426
N2	71466
Np	146427
N optimal	146427
N conservative	85158
Optimal Set	pooled_pseudo_rep
Conservative Set	rep4-rep6
Rescue Ratio	1.719474388783203
Self Consistency Ratio	1.2444239218649427
Reproducibility Test	pass

N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'