Pipeline version (latest git commit SHA1):f6730f7ec29b89176e8e9a618d1531d837f286a1 (Thu Oct 6 22:06:45 2016)

Directories and files
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FilesPath
Alignment
Replicate 1
Filtered & deduped bam ./align/rep1/SRR836458.nodup.bam
Fastq
Bam ./align/rep1/SRR836458.bam
Tag-align ./align/rep1/SRR836458.nodup.tagAlign.gz
Control 1
Filtered & deduped bam ./align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam
Fastq
Bam ./align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam
Tag-align ./align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep1/pr1/SRR836458.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep1/pr2/SRR836458.nodup.pr2.tagAlign.gz
Signal tracks
MACS2
Replicate 1
P-value ./signal/macs2/rep1/SRR836458.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/rep1/SRR836458.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw
Peaks
SPP
Replicate 1
Region peak ./peak/spp/rep1/SRR836458.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Region peak ./peak/spp/pseudo_reps/rep1/pr1/SRR836458.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
Pseudo-replicate 2
Region peak ./peak/spp/pseudo_reps/rep1/pr2/SRR836458.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
Naive overlap
Peak ./peak/SPP/overlap/SRR836458.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.gz
MACS2
Replicate 1
Narrow peak ./peak/macs2/rep1/SRR836458.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Narrow peak ./peak/macs2/pseudo_reps/rep1/pr1/SRR836458.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
Pseudo-replicate 2
Narrow peak ./peak/macs2/pseudo_reps/rep1/pr2/SRR836458.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
IDR
Pseudo-replicates
Replicate 1
IDR peak ./peak/idr/pseudo_reps/rep1/SRR836458_rep1-pr.IDR0.05.narrowPeak.gz
QC and logs
Replicate 1
BWA map. flagstat log ./qc/rep1/SRR836458.flagstat.qc
Dedup. log ./qc/rep1/SRR836458.dup.qc
PBC log ./qc/rep1/SRR836458.nodup.pbc.qc
Cross-corr. log ./qc/rep1/SRR836458.nodup.15M.cc.qc
Cross-corr. plot ./qc/rep1/SRR836458.nodup.15M.cc.plot.pdf
Control 1
BWA map. flagstat log ./qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.flagstat.qc
Dedup. log ./qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc
PBC log ./qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.pbc.qc
IDR
IDR QC log ./qc/SRR836458_IDR_final.qc
Pseudo-replicates
Replicate 1
IDR plot ./peak/idr/pseudo_reps/rep1/SRR836458_rep1-pr.unthresholded-peaks.txt.png

Visualization
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
361556780001455458140.26
ctl1
320226350002118338066.15

Dup QC (all)
 Unpaired ReadsPaired ReadsUnmapped ReadsUnpaired DupesPaired DupesPaired Opt. Dupes% Dupes
rep1
12061591001044601000.086606
ctl1
165726750013188493000.795797

Flagstat QC (all, filtered)
 Reads (QC-passed)Reads (QC-failed)Dupes (QC-passed)Dupes (QC-failed)Mapped Reads% Mapped
rep1
1101699000011016990100.00
ctl1
33841820003384182100.00

PBC QC (all)
 Total Read PairsDistinct Read PairsOne Read PairTwo Read PairsNRF = Distinct/TotalPBC1 = OnePair/DistinctPBC2 = OnePair/TwoPair
rep1
1205943411088637102445587570010.9194990.92387913.533084
ctl1
163404907720329466176412124510.4724660.6038303.844909

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
11015495950.206995956471581550.19725615000.15091091.3716441.210162

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
 

IDR QC (idr)
SRR836458_IDR_final.qc
NtN1Npconservative_setoptimal_setrescue_ratioself_consistency_ratioreproducibility
056270N/AN/ANaN1.01

rep1 pseudo-reps