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 ./align/rep1/SRR1946778.nodup.bam
Fastq
Bam ./align/rep1/SRR1946778.bam
Tag-align ./align/rep1/SRR1946778.nodup.tagAlign.gz
Replicate 2
Filtered & deduped bam ./align/rep2/SRR1946779.nodup.bam
Fastq
Bam ./align/rep2/SRR1946779.bam
Tag-align ./align/rep2/SRR1946779.nodup.tagAlign.gz
Control 1
Filtered & deduped bam ./align/ctl1/SRR1946788.nodup.bam
Fastq
Bam ./align/ctl1/SRR1946788.bam
Tag-align ./align/ctl1/SRR1946788.nodup.tagAlign.gz
Pooled replicate
Tag-align ./align/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep1/pr1/SRR1946778.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep1/pr2/SRR1946778.nodup.pr2.tagAlign.gz
Replicate 2
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep2/pr1/SRR1946779.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep2/pr2/SRR1946779.nodup.pr2.tagAlign.gz
Pooled pseudo-replicates
Pooled pseudo-replicate 1
Tag-align ./align/pooled_pseudo_reps/ppr1/SRR1946778.nodup.pr1_SRR1946779.nodup.pr1.tagAlign.gz
Pooled pseudo-replicate 2
Tag-align ./align/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign.gz
Signal tracks
MACS2
Replicate 1
P-value ./signal/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bw
Replicate 2
P-value ./signal/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bw
Pooled replicate
P-value ./signal/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.fc.signal.bw
Peaks
MACS2
Replicate 1
Narrow peak ./peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/rep1/SRR1946778.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
Replicate 2
Narrow peak ./peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/rep2/SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
Pooled replicate
Narrow peak ./peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pooled_rep/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
Pooled pseudo-replicate
Pooled pseudo-replicate 1
Broad peak ./peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.gappedPeak.gz
Pooled pseudo-replicate 2
Narrow peak ./peak/macs2/pooled_pseudo_reps/ppr2/SRR1946778.nodup.pr2_SRR1946779.nodup.pr2.tagAlign_x_SRR1946788.nodup.tagAlign.narrowPeak.gz
Naive overlap
Broad peak ./peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Gapped peak ./peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Peak ./peak/macs2/overlap/SRR1946778.nodup_SRR1946779.nodup.tagAlign_x_SRR1946788.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
QC and logs
Replicate 1
BWA map. flagstat log ./qc/rep1/SRR1946778.flagstat.qc
Dedup. log ./qc/rep1/SRR1946778.dup.qc
PBC log ./qc/rep1/SRR1946778.nodup.pbc.qc
Cross-corr. log ./qc/rep1/SRR1946778.nodup.15M.cc.qc
Cross-corr. plot ./qc/rep1/SRR1946778.nodup.15M.cc.plot.pdf
Replicate 2
BWA map. flagstat log ./qc/rep2/SRR1946779.flagstat.qc
Dedup. log ./qc/rep2/SRR1946779.dup.qc
PBC log ./qc/rep2/SRR1946779.nodup.pbc.qc
Cross-corr. log ./qc/rep2/SRR1946779.nodup.15M.cc.qc
Cross-corr. plot ./qc/rep2/SRR1946779.nodup.15M.cc.plot.pdf
Control 1
BWA map. flagstat log ./qc/ctl1/SRR1946788.flagstat.qc
Dedup. log ./qc/ctl1/SRR1946788.dup.qc
PBC log ./qc/ctl1/SRR1946788.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
610649610005967471597.72
rep2
583574820005713914497.91
ctl1
1056935010009407105489.00

Dup QC (all)
 Unpaired ReadsPaired ReadsUnmapped ReadsUnpaired DupesPaired DupesPaired Opt. Dupes% Dupes
rep1
46267633008225621000.177783
rep2
453104670011800925000.260446
ctl1
49731572006076325000.122182

Flagstat QC (all, filtered)
 Reads (QC-passed)Reads (QC-failed)Dupes (QC-passed)Dupes (QC-failed)Mapped Reads% Mapped
rep1
3804201200038042012100.00
rep2
3350954200033509542100.00
ctl1
4365524700043655247100.00

PBC QC (all)
 Total Read PairsDistinct Read PairsOne Read PairTwo Read PairsNRF = Distinct/TotalPBC1 = OnePair/DistinctPBC2 = OnePair/TwoPair
rep1
46253951384628933191136255126390.8315590.8296665.788763
rep2
45295358339793262522036067401580.7501720.7422273.741805
ctl1
49175935440136223970907638779100.8950240.90220010.239814

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
150000002550.178926314707944500.17506615000.17217641.0392032.335939
rep2
150000002750.182164001894418500.176050415000.17289121.0536342.935156

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