Pipeline version (latest git commit SHA1):1bf4068219f0dbc55eac67a562c71bdf8df0b3f4 (Wed Sep 7 02:27:13 2016)

Directories and files
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FilesPath
Alignment
Replicate 1
Filtered & deduped bam ./align/rep1/ENCFF002ABA.nodup.bam
Fastq
Bam ./align/rep1/ENCFF002ABA.bam
Tag-align ./align/rep1/ENCFF002ABA.nodup.tagAlign.gz
Replicate 2
Filtered & deduped bam ./align/rep2/H3K27acRep2.nodup.bam
Fastq .Rep2.fastq.gz
Bam ./align/rep2/H3K27acRep2.bam
Tag-align ./align/rep2/H3K27acRep2.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/ENCFF002ABA.nodup_pooled.tagAlign.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep1/pr1/ENCFF002ABA.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep1/pr2/ENCFF002ABA.nodup.pr2.tagAlign.gz
Replicate 2
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep2/pr1/H3K27acRep2.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep2/pr2/H3K27acRep2.nodup.pr2.tagAlign.gz
Pooled pseudo-replicates
Pooled pseudo-replicate 1
Tag-align ./align/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_pooled.tagAlign.gz
Pooled pseudo-replicate 2
Tag-align ./align/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_pooled.tagAlign.gz
Signal tracks
MACS2
Replicate 1
P-value ./signal/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
Replicate 2
P-value ./signal/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
Pooled replicate
P-value ./signal/macs2/pooled_rep/ENCFF002ABA.nodup_pooled.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/pooled_rep/ENCFF002ABA.nodup_pooled.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
Peaks
SPP
Pooled Replicate
Region peak ./peak/spp/pooled_rep/ENCFF002ABA.nodup_pooled.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
Replicate 1
Region peak ./peak/spp/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
Replicate 2
Region peak ./peak/spp/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
Pooled pseudo-replicates
Pooled pseudo-replicate 1
Region peak ./peak/spp/pooled_pseudo_reps/ppr1/ENCFF002ABA.nodup.pr1_pooled.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
Pooled pseudo-replicate 2
Region peak ./peak/spp/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_pooled.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
MACS2
Replicate 1
Narrow peak ./peak/macs2/rep1/ENCFF002ABA.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Replicate 2
Narrow peak ./peak/macs2/rep2/H3K27acRep2.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Pooled replicate
Narrow peak ./peak/macs2/pooled_rep/ENCFF002ABA.nodup_pooled.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Pooled pseudo-replicate
Pooled pseudo-replicate 2
Narrow peak ./peak/macs2/pooled_pseudo_reps/ppr2/ENCFF002ABA.nodup.pr2_pooled.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
Naive overlap
Peak ./peak/MACS2/overlap/ENCFF002ABA.nodup_pooled.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz
QC and logs
Replicate 1
BWA map. flagstat log ./qc/rep1/ENCFF002ABA.flagstat.qc
Dedup. log ./qc/rep1/ENCFF002ABA.dup.qc
PBC log ./qc/rep1/ENCFF002ABA.nodup.pbc.qc
Cross-corr. log ./qc/rep1/ENCFF002ABA.nodup.15M.cc.qc
Cross-corr. plot ./qc/rep1/ENCFF002ABA.nodup.15M.cc.plot.pdf
Replicate 2
BWA map. flagstat log ./qc/rep2/H3K27acRep2.flagstat.qc
Dedup. log ./qc/rep2/H3K27acRep2.dup.qc
PBC log ./qc/rep2/H3K27acRep2.nodup.pbc.qc
Cross-corr. log ./qc/rep2/H3K27acRep2.nodup.15M.cc.qc
Cross-corr. plot ./qc/rep2/H3K27acRep2.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

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
6421982000628864597.92
rep2
176394350001728946198.02
ctl1
175604270001587066790.38

Dup QC (all)
 Unpaired ReadsPaired ReadsUnmapped ReadsUnpaired DupesPaired DupesPaired Opt. Dupes% Dupes
rep1
521671000331110000.063471
rep2
13556542001121334000.082715
ctl1
1163907600171193000.014708

Flagstat QC (all, filtered)
 Reads (QC-passed)Reads (QC-failed)Dupes (QC-passed)Dupes (QC-failed)Mapped Reads% Mapped
rep1
48856000004885600100.00
rep2
1243520800012435208100.00
ctl1
1146788300011467883100.00

PBC QC (all)
 Total Read PairsDistinct Read PairsOne Read PairTwo Read PairsNRF = Distinct/TotalPBC1 = OnePair/DistinctPBC2 = OnePair/TwoPair
rep1
5214208488383545826232749810.9366400.93832516.665235
rep2
1354644712430568114072949400330.9176260.91768112.134993
ctl1
1160961411458969113117801449420.9870240.98715578.043493

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
48834502400.194761782710308400.155268915000.096497072.0183181.67197
rep2
124291251650.179335683186069400.171572515000.15535551.1543571.478706

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