Pipeline version (latest git commit SHA1):ba549bcd70f73d261f452659301ef1ae1a1ae4ff (Mon Jan 30 20:26:58 2017)

Directories and files
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FilesPath
Alignment
Replicate 1
Filtered & deduped bam ./align/rep1/SRR1016005.nodup.bam
Fastq
Bam ./align/rep1/SRR1016005.bam
Tag-align ./align/rep1/SRR1016005.nodup.tagAlign.gz
Replicate 2
Filtered & deduped bam ./align/rep2/SRR1016008.nodup.bam
Fastq
Bam ./align/rep2/SRR1016008.bam
Tag-align ./align/rep2/SRR1016008.nodup.tagAlign.gz
Control 1
Filtered & deduped bam ./align/ctl1/ENCFF001HNC.nodup.bam
Fastq
Bam ./align/ctl1/ENCFF001HNC.bam
Tag-align ./align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
Pooled replicate
Tag-align ./align/pooled_rep/SRR1016005.nodup_SRR1016008.nodup.tagAlign.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep1/pr1/SRR1016005.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep1/pr2/SRR1016005.nodup.pr2.tagAlign.gz
Replicate 2
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep2/pr1/SRR1016008.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep2/pr2/SRR1016008.nodup.pr2.tagAlign.gz
Pooled pseudo-replicates
Pooled pseudo-replicate 1
Tag-align ./align/pooled_pseudo_reps/ppr1/SRR1016005.nodup.pr1_SRR1016008.nodup.pr1.tagAlign.gz
Pooled pseudo-replicate 2
Tag-align ./align/pooled_pseudo_reps/ppr2/SRR1016005.nodup.pr2_SRR1016008.nodup.pr2.tagAlign.gz
Signal tracks
MACS2
Replicate 1
P-value ./signal/macs2/rep1/SRR1016005.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/rep1/SRR1016005.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
Replicate 2
P-value ./signal/macs2/rep2/SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/rep2/SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
Pooled replicate
P-value ./signal/macs2/pooled_rep/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/pooled_rep/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
Peaks
SPP
Pooled Replicate
Region peak ./peak/spp/pooled_rep/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
Replicate 1
Region peak ./peak/spp/rep1/SRR1016005.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
Replicate 2
Region peak ./peak/spp/rep2/SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
Pooled pseudo-replicates
Pooled pseudo-replicate 1
Region peak ./peak/spp/pooled_pseudo_reps/ppr1/SRR1016005.nodup.pr1_SRR1016008.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
Pooled pseudo-replicate 2
Region peak ./peak/spp/pooled_pseudo_reps/ppr2/SRR1016005.nodup.pr2_SRR1016008.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
Naive overlap
Peak ./peak/spp/overlap/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.regionPeak.gz
MACS2
Replicate 1
Narrow peak ./peak/macs2/rep1/SRR1016005.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/rep1/SRR1016005.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/rep1/SRR1016005.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
Replicate 2
Narrow peak ./peak/macs2/rep2/SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/rep2/SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/rep2/SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
Pooled replicate
Narrow peak ./peak/macs2/pooled_rep/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/pooled_rep/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pooled_rep/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
Pooled pseudo-replicate
Pooled pseudo-replicate 1
Broad peak ./peak/macs2/pooled_pseudo_reps/ppr2/SRR1016005.nodup.pr2_SRR1016008.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pooled_pseudo_reps/ppr2/SRR1016005.nodup.pr2_SRR1016008.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
Pooled pseudo-replicate 2
Narrow peak ./peak/macs2/pooled_pseudo_reps/ppr2/SRR1016005.nodup.pr2_SRR1016008.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
IDR
True replicates
Rep. 1 vs. Rep. 2
IDR peak ./peak/idr/true_reps/rep1-rep2/POL2RA_rep1-rep2.IDR0.05.filt.narrowPeak.gz
Pooled pseudo-replicates
IDR peak ./peak/idr/pooled_pseudo_reps/POL2RA_ppr.IDR0.05.filt.narrowPeak.gz
Optimal set
IDR peak ./peak/idr/optimal_set/POL2RA_ppr.IDR0.05.filt.narrowPeak.gz
Conservative set
IDR peak ./peak/idr/conservative_set/POL2RA_rep1-rep2.IDR0.05.filt.narrowPeak.gz
QC and logs
Replicate 1
BWA map. flagstat log ./qc/rep1/SRR1016005.flagstat.qc
Dedup. log ./qc/rep1/SRR1016005.dup.qc
PBC log ./qc/rep1/SRR1016005.nodup.pbc.qc
Cross-corr. log ./qc/rep1/SRR1016005.nodup.15M.cc.qc
Cross-corr. plot ./qc/rep1/SRR1016005.nodup.15M.cc.plot.pdf
Replicate 2
BWA map. flagstat log ./qc/rep2/SRR1016008.flagstat.qc
Dedup. log ./qc/rep2/SRR1016008.dup.qc
PBC log ./qc/rep2/SRR1016008.nodup.pbc.qc
Cross-corr. log ./qc/rep2/SRR1016008.nodup.15M.cc.qc
Cross-corr. plot ./qc/rep2/SRR1016008.nodup.15M.cc.plot.pdf
Control 1
BWA map. flagstat log ./qc/ctl1/ENCFF001HNC.flagstat.qc
Dedup. log ./qc/ctl1/ENCFF001HNC.dup.qc
PBC log ./qc/ctl1/ENCFF001HNC.nodup.pbc.qc
IDR
IDR QC log ./qc/POL2RA_IDR_final.qc
True replicates
Rep. 1 vs. Rep. 2
IDR plot ./peak/idr/true_reps/rep1-rep2/POL2RA_rep1-rep2.unthresholded-peaks.txt.png
Pooled pseudo-replicates
IDR plot ./peak/idr/pooled_pseudo_reps/POL2RA_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)


Flagstat QC (all)
 Reads (QC-passed)Reads (QC-failed)Dupes (QC-passed)Dupes (QC-failed)Mapped Reads% Mapped
rep1
236331260002042466486.42
rep2
204305230001958214995.85
ctl1
175604270001587350190.39

Dup QC (all)
 Unpaired ReadsPaired ReadsUnmapped ReadsUnpaired DupesPaired DupesPaired Opt. Dupes% Dupes
rep1
1716447500256592000.014949
rep2
15774786001510594000.09576
ctl1
1136900200167589000.014741

Flagstat QC (all, filtered)
 Reads (QC-passed)Reads (QC-failed)Dupes (QC-passed)Dupes (QC-failed)Mapped Reads% Mapped
rep1
1690788300016907883100.00
rep2
1426419200014264192100.00
ctl1
1120141300011201413100.00

PBC QC (all)
 Total Read PairsDistinct Read PairsOne Read PairTwo Read PairsNRF = Distinct/TotalPBC1 = OnePair/DistinctPBC2 = OnePair/TwoPair
rep1
1711158916960261168177431379060.9911560.991597121.950771
rep2
15766935143688371311657411305420.9113270.91284911.602023
ctl1
1133953511192492110488141414680.9870330.98716378.101154

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

  • 0-0.5 is severe bottlenecking
  • 0.5-0.8 is moderate bottlenecking
  • 0.8-0.9 is mild bottlenecking
  • 0.9-1.0 is no bottlenecking


Cross-correlation QC (all)
 numReadsestFragLencorr_estFragLenPhantomPeakcorr_phantomPeakargmin_corrmin_corrNSCRSC
rep1
150000001500.188645062407594750.187541315000.17482231.0790681.086783
rep2
142584111550.277721043875615550.263236615000.171621.6182321.158099

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)
POL2RA_IDR_final.qc
NtNpconservative_setoptimal_setrescue_ratioself_consistency_ratioreproducibility
1950024377rep1-rep2pooled_pseudo_rep1.250102564102564NaN1

true reps (rep1-rep2)
 
pooled pseudo-reps