Directories and files
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FilesPath
Alignment
Replicate 1
trimmed fastq1 ./align/rep1/ATAC21-trimmed-pair1.trim.fastq.gz
trimmed fastq2 ./align/rep1/ATAC21-trimmed-pair2.trim.fastq.gz
bam ./align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.bam
filtered bam ./align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bam
bedpe ./align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
tagalign ./align/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Replicate 2
trimmed fastq1 ./align/rep2/ATAC22-trimmed-pair1.trim.fastq.gz
trimmed fastq2 ./align/rep2/ATAC22-trimmed-pair2.trim.fastq.gz
bam ./align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.bam
filtered bam ./align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bam
bedpe ./align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.bedpe.gz
tagalign ./align/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tagAlign.gz
Signal tracks
MACS2
Replicate 1
p-value ./signal/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig
fold enrichment ./signal/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
Replicate 2
p-value ./signal/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.fc.signal.bigwig
fold enrichment ./signal/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval.signal.bigwig
Pooled replicate
p-value ./signal/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.fc.signal.bigwig
fold enrichment ./signal/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval.signal.bigwig
Peaks
IDR
True replicates
Rep. 1 vs Rep. 2
IDR peak ./peak/idr/true_reps/rep1-rep2/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Unthresholded IDR peak ./peak/idr/true_reps/rep1-rep2/rep1-rep2.unthresholded-peaks.txt.gz
Optimal set
IDR peak ./peak/idr/optimal_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
Conservative set
IDR peak ./peak/idr/conservative_set/rep1-rep2.IDR0.1.filt.narrowPeak.gz
MACS2
Replicate 1
gapped peak (p-val thld: 0.01) ./peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz
gapped peak ./peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
peak ./peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
peak (p-val thld: 0.01) ./peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
filtered peak ./peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
filtered gapped peak ./peak/macs2/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
Replicate 2
gapped peak (p-val thld: 0.01) ./peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.gappedPeak.gz
gapped peak ./peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.gappedPeak.gz
peak ./peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.narrowPeak.gz
peak (p-val thld: 0.01) ./peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.narrowPeak.gz
filtered peak ./peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.narrowPeak.gz
filtered gapped peak ./peak/macs2/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.17.tn5.pf.pval0.1.500000.gappedPeak.gz
Pooled replicate
gapped peak (p-val thld: 0.01) ./peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.gappedPeak.gz
gapped peak ./peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.gappedPeak.gz
peak ./peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.narrowPeak.gz
peak (p-val thld: 0.01) ./peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.narrowPeak.gz
filtered peak ./peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.narrowPeak.gz
filtered gapped peak ./peak/macs2/pooled_rep/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.gappedPeak.gz
Naive overlap
peak ./peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.gz
gapped peak ./peak/macs2/overlap/ATAC21-trimmed-pair1.trim.PE2SE.nodup.17.tn5_pooled.pf.pval0.1.500000.naive_overlap.gappedPeak.gz
QC and logs
Replicate 1
bowtie2 QC ./qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.align.log
dup. QC ./qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.dup.qc
map QC ./qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc
PBC QC ./qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
cross-corr. QC ./qc/rep1/ATAC21-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc
ATAQC ./qc/rep1/ATAC21-trimmed-pair1.PE2SE_qc.html
Replicate 2
bowtie2 QC ./qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.align.log
dup. QC ./qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.dup.qc
map QC ./qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc
PBC QC ./qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
cross-corr. QC ./qc/rep2/ATAC22-trimmed-pair1.trim.PE2SE.nodup.25.cc.qc
ATAQC ./qc/rep2/ATAC22-trimmed-pair1.PE2SE_qc.html
IDR QC ./qc/IDR_final.qc

Visualization (add -url_base [URL_ROOT_DIR_FOR_OUT_DIR] to the command line.)
Visualize  JSON (datahub)

Workflow diagram (rep : Replicate, ctl : Control, pr : Pseudo-replicate, ppr : Pooled pseudo-replicate)


Bowtie2 QC (all)
 Total Reads% Aligned
rep1
21273893895.68
rep2
8923286294.72

Dup QC (all)
 Unpaired ReadsPaired ReadsUnmapped ReadsUnpaired DupesPaired DupesPaired Opt. Dupes% Dupes
rep1
01543427410071550575624705780.463582
rep2
0642934920025048543215523840.389597

Flagstat QC (all, filtered)
 Reads (QC-passed)Reads (QC-failed)Dupes (QC-passed)Dupes (QC-failed)Mapped Reads% Mapped
rep1
165584332000165584332100.00
rep2
7848989800078489898100.00

PBC QC (all)
 Total Read PairsDistinct Read PairsOne Read PairTwo Read PairsNRF = Distinct/TotalPBC1 = OnePair/DistinctPBC2 = OnePair/TwoPair
rep1
1030591918161969965132263130957930.7919690.7979974.973526
rep2
44295404383549583339888643100130.8658900.8707847.749138

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
2500000000.265560858672526550.267621315000.24801351.0707520.89491630
rep2
2500000000.265230395730548550.267132715000.24813711.0688860.89985370

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)
IDR_final.qc
NtNpconservative_setoptimal_setrescue_ratioself_consistency_ratioreproducibility
835450rep1-rep2rep1-rep2InfinityNaN0

true reps (rep1-rep2)