Title: ZNF467_MACS2

Report generated at Thu Apr 13 18:47:17 PDT 2017

Command line arguments

-title ZNF467_MACS2 -nth 5 -species hg38 -url_base http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF467_MACS2/out -tag1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz -ctl_tag /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -histone

Pipeline version

Latest git commit SHA1: 3e6c43ca5035c8766d19e6245573946c380bb5a8 (Sat Apr 8 15:37:52 2017)


Directories and files
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FilesPath
Alignment
Replicate 1
Tag-align /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz
Control 1
Tag-align /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign.gz
Signal tracks
MACS2
Replicate 1
P-value ./signal/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
Peaks
MACS2
Replicate 1
Narrow peak ./peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Narrow peak ./peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
Pseudo-replicate 2
Narrow peak ./peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
Naive overlap
Broad peak ./peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.broadPeak.gz
Gapped peak ./peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.gappedPeak.gz
Peak ./peak/macs2/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.narrowPeak.gz
QC and logs
Replicate 1
Cross-corr. log ./qc/rep1/SRR1370886_1.nodup.15M.cc.qc
Cross-corr. plot ./qc/rep1/SRR1370886_1.nodup.15M.cc.plot.pdf

Visualization
Visualize  JSON (datahub)

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


Enrichment QC (strand cross-correlation measures)
Reads15000000
Est. Fragment Len.145
Corr. Est. Fragment Len.0.266724316314493
Phantom Peak55
Corr. Phantom Peak0.2289182
Argmin. Corr.1500
Min. Corr.0.1735547
NSC1.536832
RSC1.682869

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


rep1