Pipeline version (latest git commit SHA1):8a3b319340f2e0ff23f69e8fe7df7c56f75828c1 (Mon Jan 23 10:50:55 2017)

Directories and files
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Alignment
Replicate 1
Tag-align ./align/rep1/Polstein2015_MergedRep1.nodup.tagAlign.gz
Replicate 2
Tag-align ./align/rep2/Polstein2015_MergedRep2.nodup.tagAlign.gz
Pooled replicate
Tag-align ./align/pooled_rep/Polstein2015_MergedRep1.nodup_Polstein2015_MergedRep2.nodup.tagAlign.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep1/pr1/Polstein2015_MergedRep1.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep1/pr2/Polstein2015_MergedRep1.nodup.pr2.tagAlign.gz
Replicate 2
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep2/pr1/Polstein2015_MergedRep2.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep2/pr2/Polstein2015_MergedRep2.nodup.pr2.tagAlign.gz
Pooled pseudo-replicates
Pooled pseudo-replicate 1
Tag-align ./align/pooled_pseudo_reps/ppr1/Polstein2015_MergedRep1.nodup.pr1_Polstein2015_MergedRep2.nodup.pr1.tagAlign.gz
Pooled pseudo-replicate 2
Tag-align ./align/pooled_pseudo_reps/ppr2/Polstein2015_MergedRep1.nodup.pr2_Polstein2015_MergedRep2.nodup.pr2.tagAlign.gz
Signal tracks
MACS2
Replicate 1
P-value ./signal/macs2/rep1/Polstein2015_MergedRep1.nodup.pf.pval.signal.bigwig
Fold enrichment ./signal/macs2/rep1/Polstein2015_MergedRep1.nodup.pf.fc.signal.bigwig
Replicate 2
P-value ./signal/macs2/rep2/Polstein2015_MergedRep2.nodup.pf.pval.signal.bigwig
Fold enrichment ./signal/macs2/rep2/Polstein2015_MergedRep2.nodup.pf.fc.signal.bigwig
Pooled replicate
P-value ./signal/macs2/pooled_rep/Polstein2015_MergedRep1.nodup_Polstein2015_MergedRep2.nodup.pf.pval.signal.bigwig
Fold enrichment ./signal/macs2/pooled_rep/Polstein2015_MergedRep1.nodup_Polstein2015_MergedRep2.nodup.pf.fc.signal.bigwig
Peaks
MACS2
Replicate 1
Gapped peak (p-val thresh=.01) ./peak/macs2/rep1/Polstein2015_MergedRep1.nodup.pf.gappedPeak.gz
Narrow peak (p-val thresh=.01) ./peak/macs2/rep1/Polstein2015_MergedRep1.nodup.pf.narrowPeak.gz
Narrow peak ./peak/macs2/rep1/Polstein2015_MergedRep1.nodup.pf.pval0.1.narrowPeak.gz
Gapped peak ./peak/macs2/rep1/Polstein2015_MergedRep1.nodup.pf.pval0.1.gappedPeak.gz
Filtered narrow peak ./peak/macs2/rep1/Polstein2015_MergedRep1.nodup.pf.pval0.1.500K.narrowPeak.gz
Filtered gapped peak ./peak/macs2/rep1/Polstein2015_MergedRep1.nodup.pf.pval0.1.500K.gappedPeak.gz
Replicate 2
Gapped peak (p-val thresh=.01) ./peak/macs2/rep2/Polstein2015_MergedRep2.nodup.pf.gappedPeak.gz
Narrow peak (p-val thresh=.01) ./peak/macs2/rep2/Polstein2015_MergedRep2.nodup.pf.narrowPeak.gz
Narrow peak ./peak/macs2/rep2/Polstein2015_MergedRep2.nodup.pf.pval0.1.narrowPeak.gz
Gapped peak ./peak/macs2/rep2/Polstein2015_MergedRep2.nodup.pf.pval0.1.gappedPeak.gz
Filtered narrow peak ./peak/macs2/rep2/Polstein2015_MergedRep2.nodup.pf.pval0.1.500K.narrowPeak.gz
Filtered gapped peak ./peak/macs2/rep2/Polstein2015_MergedRep2.nodup.pf.pval0.1.500K.gappedPeak.gz
Pooled replicate
Gapped peak (p-val thresh=.01) ./peak/macs2/pooled_rep/Polstein2015_MergedRep1.nodup_Polstein2015_MergedRep2.nodup.pf.gappedPeak.gz
Narrow peak (p-val thresh=.01) ./peak/macs2/pooled_rep/Polstein2015_MergedRep1.nodup_Polstein2015_MergedRep2.nodup.pf.narrowPeak.gz
Narrow peak ./peak/macs2/pooled_rep/Polstein2015_MergedRep1.nodup_Polstein2015_MergedRep2.nodup.pf.pval0.1.narrowPeak.gz
Gapped peak ./peak/macs2/pooled_rep/Polstein2015_MergedRep1.nodup_Polstein2015_MergedRep2.nodup.pf.pval0.1.gappedPeak.gz
Filtered narrow peak ./peak/macs2/pooled_rep/Polstein2015_MergedRep1.nodup_Polstein2015_MergedRep2.nodup.pf.pval0.1.500K.narrowPeak.gz
Filtered gapped peak ./peak/macs2/pooled_rep/Polstein2015_MergedRep1.nodup_Polstein2015_MergedRep2.nodup.pf.pval0.1.500K.gappedPeak.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Narrow peak ./peak/macs2/pseudo_reps/rep1/pr1/Polstein2015_MergedRep1.nodup.pr1.pf.pval0.1.narrowPeak.gz
Gapped peak ./peak/macs2/pseudo_reps/rep1/pr1/Polstein2015_MergedRep1.nodup.pr1.pf.pval0.1.gappedPeak.gz
Filtered narrow peak ./peak/macs2/pseudo_reps/rep1/pr1/Polstein2015_MergedRep1.nodup.pr1.pf.pval0.1.500K.narrowPeak.gz
Filtered gapped peak ./peak/macs2/pseudo_reps/rep1/pr1/Polstein2015_MergedRep1.nodup.pr1.pf.pval0.1.500K.gappedPeak.gz
Pseudo-replicate 2
Narrow peak ./peak/macs2/pseudo_reps/rep1/pr2/Polstein2015_MergedRep1.nodup.pr2.pf.pval0.1.narrowPeak.gz
Gapped peak ./peak/macs2/pseudo_reps/rep1/pr2/Polstein2015_MergedRep1.nodup.pr2.pf.pval0.1.gappedPeak.gz
Filtered narrow peak ./peak/macs2/pseudo_reps/rep1/pr2/Polstein2015_MergedRep1.nodup.pr2.pf.pval0.1.500K.narrowPeak.gz
Filtered gapped peak ./peak/macs2/pseudo_reps/rep1/pr2/Polstein2015_MergedRep1.nodup.pr2.pf.pval0.1.500K.gappedPeak.gz
Replicate 2
Pseudo-replicate 1
Narrow peak ./peak/macs2/pseudo_reps/rep2/pr1/Polstein2015_MergedRep2.nodup.pr1.pf.pval0.1.narrowPeak.gz
Gapped peak ./peak/macs2/pseudo_reps/rep2/pr1/Polstein2015_MergedRep2.nodup.pr1.pf.pval0.1.gappedPeak.gz
Filtered narrow peak ./peak/macs2/pseudo_reps/rep2/pr1/Polstein2015_MergedRep2.nodup.pr1.pf.pval0.1.500K.narrowPeak.gz
Filtered gapped peak ./peak/macs2/pseudo_reps/rep2/pr1/Polstein2015_MergedRep2.nodup.pr1.pf.pval0.1.500K.gappedPeak.gz
Pseudo-replicate 2
Narrow peak ./peak/macs2/pseudo_reps/rep2/pr2/Polstein2015_MergedRep2.nodup.pr2.pf.pval0.1.narrowPeak.gz
Gapped peak ./peak/macs2/pseudo_reps/rep2/pr2/Polstein2015_MergedRep2.nodup.pr2.pf.pval0.1.gappedPeak.gz
Filtered narrow peak ./peak/macs2/pseudo_reps/rep2/pr2/Polstein2015_MergedRep2.nodup.pr2.pf.pval0.1.500K.narrowPeak.gz
Filtered gapped peak ./peak/macs2/pseudo_reps/rep2/pr2/Polstein2015_MergedRep2.nodup.pr2.pf.pval0.1.500K.gappedPeak.gz
Pooled pseudo-replicates
Pooled pseudo-replicate 1
Narrow peak ./peak/macs2/pooled_pseudo_reps/ppr1/Polstein2015_MergedRep1.nodup.pr1_Polstein2015_MergedRep2.nodup.pr1.pf.pval0.1.narrowPeak.gz
Gapped peak ./peak/macs2/pooled_pseudo_reps/ppr1/Polstein2015_MergedRep1.nodup.pr1_Polstein2015_MergedRep2.nodup.pr1.pf.pval0.1.gappedPeak.gz
Filtered narrow peak ./peak/macs2/pooled_pseudo_reps/ppr1/Polstein2015_MergedRep1.nodup.pr1_Polstein2015_MergedRep2.nodup.pr1.pf.pval0.1.500K.narrowPeak.gz
Filtered gapped peak ./peak/macs2/pooled_pseudo_reps/ppr1/Polstein2015_MergedRep1.nodup.pr1_Polstein2015_MergedRep2.nodup.pr1.pf.pval0.1.500K.gappedPeak.gz
Pooled pseudo-replicate 2
Narrow peak ./peak/macs2/pooled_pseudo_reps/ppr2/Polstein2015_MergedRep1.nodup.pr2_Polstein2015_MergedRep2.nodup.pr2.pf.pval0.1.narrowPeak.gz
Gapped peak ./peak/macs2/pooled_pseudo_reps/ppr2/Polstein2015_MergedRep1.nodup.pr2_Polstein2015_MergedRep2.nodup.pr2.pf.pval0.1.gappedPeak.gz
Filtered narrow peak ./peak/macs2/pooled_pseudo_reps/ppr2/Polstein2015_MergedRep1.nodup.pr2_Polstein2015_MergedRep2.nodup.pr2.pf.pval0.1.500K.narrowPeak.gz
Filtered gapped peak ./peak/macs2/pooled_pseudo_reps/ppr2/Polstein2015_MergedRep1.nodup.pr2_Polstein2015_MergedRep2.nodup.pr2.pf.pval0.1.500K.gappedPeak.gz
Naive overlap
Narrow peak ./peak/macs2/overlap/Polstein2015_MergedRep1.nodup_Polstein2015_MergedRep2.nodup.pf.pval0.1.500K.naive_overlap.filt.narrowPeak.gz
Gapped peak ./peak/macs2/overlap/Polstein2015_MergedRep1.nodup_Polstein2015_MergedRep2.nodup.pf.pval0.1.500K.naive_overlap.filt.gappedPeak.gz
IDR
True replicates
Rep. 1 vs. Rep. 2
IDR peak ./peak/idr/true_reps/rep1-rep2/Polstein2015_MergedReps_rep1-rep2.IDR0.1.filt.narrowPeak.gz
Pseudo-replicates
Replicate 1
IDR peak ./peak/idr/pseudo_reps/rep1/Polstein2015_MergedReps_rep1-pr.IDR0.1.filt.narrowPeak.gz
Replicate 2
IDR peak ./peak/idr/pseudo_reps/rep2/Polstein2015_MergedReps_rep2-pr.IDR0.1.filt.narrowPeak.gz
Pooled pseudo-replicates
IDR peak ./peak/idr/pooled_pseudo_reps/Polstein2015_MergedReps_ppr.IDR0.1.filt.narrowPeak.gz
Optimal set
IDR peak ./peak/idr/optimal_set/Polstein2015_MergedReps_rep1-rep2.IDR0.1.filt.narrowPeak.gz
Conservative set
IDR peak ./peak/idr/conservative_set/Polstein2015_MergedReps_rep1-rep2.IDR0.1.filt.narrowPeak.gz
QC and logs
Replicate 1
Cross-corr. plot ./qc/rep1/Polstein2015_MergedRep1.nodup.25M.cc.plot.pdf
Replicate 2
Cross-corr. plot ./qc/rep2/Polstein2015_MergedRep2.nodup.25M.cc.plot.pdf
IDR
IDR QC log ./qc/Polstein2015_MergedReps_IDR_final.qc
True replicates
Rep. 1 vs. Rep. 2
IDR plot ./peak/idr/true_reps/rep1-rep2/Polstein2015_MergedReps_rep1-rep2.unthresholded-peaks.txt.png
Pseudo-replicates
Replicate 1
IDR plot ./peak/idr/pseudo_reps/rep1/Polstein2015_MergedReps_rep1-pr.unthresholded-peaks.txt.png
Replicate 2
IDR plot ./peak/idr/pseudo_reps/rep2/Polstein2015_MergedReps_rep2-pr.unthresholded-peaks.txt.png
Pooled pseudo-replicates
IDR plot ./peak/idr/pooled_pseudo_reps/Polstein2015_MergedReps_ppr.unthresholded-peaks.txt.png

Visualization (add -url_base [URL_ROOT_DIR_FOR_OUT_DIR] to the command line.)
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
2500000000.311273423535483200.3067515000.24817961.2542261.077231
rep2
2500000000.301690195269587200.299252115000.24276461.2427271.043162

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)
Polstein2015_MergedReps_IDR_final.qc
NtN1N2Npconservative_setoptimal_setrescue_ratioself_consistency_ratioreproducibility
132211108067108009129153rep1-rep2rep1-rep21.02367734392542191.00053699228767971

true reps (rep1-rep2)
 
rep1 pseudo-reps
 
rep2 pseudo-reps
 
pooled pseudo-reps