Directories and files
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FilesPath
Replicate 1 (rep1)./align_rep1
fastq
bam./align_rep1/primarykeratinocyte_d6.GGR.Stanford_Snyder.b2.t1_S6_L001_R1_001.bam
filtered bam./align_rep1/primarykeratinocyte_d6.GGR.Stanford_Snyder.b2.t1_S6_L001_R1_001.nodup.bam
tagalign./align_rep1/primarykeratinocyte_d6.GGR.Stanford_Snyder.b2.t1_S6_L001_R1_001.nodup.tagAlign.gz
Signal track
pval (macs2, rep1)./peaks_macs2/true_replicates/primarykeratinocyte_d6.GGR.Stanford_Snyder.b2.t1_S6_L001_R1_001.nodup.pval.signal.bw
fc (macs2, rep1)./peaks_macs2/true_replicates/primarykeratinocyte_d6.GGR.Stanford_Snyder.b2.t1_S6_L001_R1_001.nodup.fc.signal.bw
Peaks./peaks_macs2
True replicates./peaks_macs2/true_replicates
rep1./peaks_macs2/true_replicates/primarykeratinocyte_d6.GGR.Stanford_Snyder.b2.t1_S6_L001_R1_001.nodup.narrowPeak.gz

Visualization
Visualize  JSON (datahub)

Workflow diagram


Flagstat QC (all)
 Reads (QC-passed)Reads (QC-failed)Dupes (QC-passed)Dupes (QC-failed)Mapped Reads% Mapped
rep1
4348729000422784897.22

Dup QC (all)
 Unpaired ReadsPaired ReadsUnmapped ReadsUnpaired DupesPaired DupesPaired Opt. Dupes% Dupes
rep1
39067520019715000.005046

Flagstat QC (all, filtered)
 Reads (QC-passed)Reads (QC-failed)Dupes (QC-passed)Dupes (QC-failed)Mapped Reads% Mapped
rep1
38870370003887037100.00

PBC QC (all)
 Total Read PairsDistinct Read PairsOne Read PairTwo Read PairsNRF = Distinct/TotalPBC1 = OnePair/DistinctPBC2 = OnePair/TwoPair
rep1
390194438829773866206159520.9951390.995681242.364970

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_corrphantomPeakCoefrelPhantomPeakCoefQualityTag
rep1
38828362550.0606967427174944750.0600187615000.055080071.1019731.1372811

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