Pipeline version (latest git commit SHA1):c98662939a310709da28f62bacfb896089a35342 (Tue Jan 10 09:44:38 2017)

Directories and files
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FilesPath
Alignment
Replicate 1
Filtered & deduped bam
Tag-align ./align/rep1/ZFP64_Rep1.nodup.tagAlign.gz
Replicate 2
Filtered & deduped bam
Tag-align ./align/rep2/ZFP64_Rep2.nodup.tagAlign.gz
Control 1
Tag-align
Pooled replicate
Tag-align ./align/pooled_rep/ZFP64_Rep1.nodup_ZFP64_Rep2.nodup.tagAlign.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep1/pr1/ZFP64_Rep1.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep1/pr2/ZFP64_Rep1.nodup.pr2.tagAlign.gz
Replicate 2
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep2/pr1/ZFP64_Rep2.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep2/pr2/ZFP64_Rep2.nodup.pr2.tagAlign.gz
Pooled pseudo-replicates
Pooled pseudo-replicate 1
Tag-align ./align/pooled_pseudo_reps/ppr1/ZFP64_Rep1.nodup.pr1_ZFP64_Rep2.nodup.pr1.tagAlign.gz
Pooled pseudo-replicate 2
Tag-align ./align/pooled_pseudo_reps/ppr2/ZFP64_Rep1.nodup.pr2_ZFP64_Rep2.nodup.pr2.tagAlign.gz
Signal tracks
MACS2
Pooled replicate
P-value ./signal/macs2/pooled_rep/ZFP64_Rep1.nodup_ZFP64_Rep2.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/pooled_rep/ZFP64_Rep1.nodup_ZFP64_Rep2.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
Peaks
SPP
Pooled Replicate
Region peak ./peak/spp/pooled_rep/ZFP64_Rep1.nodup_ZFP64_Rep2.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Replicate 1
Region peak ./peak/spp/rep1/ZFP64_Rep1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Replicate 2
Region peak ./peak/spp/rep2/ZFP64_Rep2.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Pooled pseudo-replicates
Pooled pseudo-replicate 1
Region peak ./peak/spp/pooled_pseudo_reps/ppr1/ZFP64_Rep1.nodup.pr1_ZFP64_Rep2.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Pooled pseudo-replicate 2
Region peak ./peak/spp/pooled_pseudo_reps/ppr2/ZFP64_Rep1.nodup.pr2_ZFP64_Rep2.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Naive overlap
Peak ./peak/spp/overlap/ZFP64_Rep1.nodup_ZFP64_Rep2.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
MACS2
Pooled replicate
Narrow peak ./peak/macs2/pooled_rep/ZFP64_Rep1.nodup_ZFP64_Rep2.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/pooled_rep/ZFP64_Rep1.nodup_ZFP64_Rep2.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pooled_rep/ZFP64_Rep1.nodup_ZFP64_Rep2.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
IDR
True replicates
Rep. 1 vs. Rep. 2
IDR peak ./peak/idr/true_reps/rep1-rep2/ZFP64_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Pooled pseudo-replicates
IDR peak ./peak/idr/pooled_pseudo_reps/ZFP64_ppr.IDR0.05.filt.narrowPeak.gz
Optimal set
IDR peak ./peak/idr/optimal_set/ZFP64_ppr.IDR0.05.filt.narrowPeak.gz
Conservative set
IDR peak ./peak/idr/conservative_set/ZFP64_rep1-rep2.IDR0.05.filt.narrowPeak.gz
QC and logs
Replicate 1
Cross-corr. log ./qc/rep1/ZFP64_Rep1.nodup.15M.cc.qc
Cross-corr. plot ./qc/rep1/ZFP64_Rep1.nodup.15M.cc.plot.pdf
Replicate 2
Cross-corr. log ./qc/rep2/ZFP64_Rep2.nodup.15M.cc.qc
Cross-corr. plot ./qc/rep2/ZFP64_Rep2.nodup.15M.cc.plot.pdf
IDR
IDR QC log ./qc/ZFP64_IDR_final.qc
True replicates
Rep. 1 vs. Rep. 2
IDR plot ./peak/idr/true_reps/rep1-rep2/ZFP64_rep1-rep2.unthresholded-peaks.txt.png
Pooled pseudo-replicates
IDR plot ./peak/idr/pooled_pseudo_reps/ZFP64_ppr.unthresholded-peaks.txt.png

Visualization
Visualize  JSON (datahub)

Workflow diagram (g. peak : gapped peak from MACS2, n. peak : narrow peak from MACS2, r. peak : region peak from SPP)


Cross-correlation QC (all)
 numReadsestFragLencorr_estFragLenPhantomPeakcorr_phantomPeakargmin_corrmin_corrNSCRSC
rep1
93487461500.161867861463698550.148015115000.12146051.3326791.521669
rep2
150000001500.264589517599431550.237848215000.18619521.4210331.51771

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
Important columns highlighted, but all/whole file can be stored for display


rep1
 
rep2
 

IDR QC (idr)
ZFP64_IDR_final.qc
NtNpconservative_setoptimal_setrescue_ratioself_consistency_ratioreproducibility
3103735553rep1-rep2pooled_pseudo_rep1.1455037535844315NaN1

true reps (rep1-rep2)
 
pooled pseudo-reps