Title: rbc_h5

Report generated at Wed Aug 25 20:03:09 +07 2021

Command line arguments

-type histone -out_dir /mnt/scratch/ws/manuriddinov/202109231429EVL24//Vertebrates/Chicken -title rbc_h5 -pe -species galGal5 -system local -nth 23 -bam1 /mnt/scratch/ws/manuriddinov/202109231429EVL24//Vertebrates/Chicken/Chickseq/RBC_I_rep1.sort.bam -ctl_bam1 /mnt/scratch/ws/manuriddinov/202109231429EVL24//Vertebrates/Chicken/Chickseq/RBC_I_contrl.sort.bam

Pipeline version

Latest git commit SHA1: 0816591bacf8737379027eb3d45cd45170cfe246 (Wed Jun 6 01:27:19 2018)


Directories and files
Expand all   Collapse all
FilesPath
Alignment .
Replicate 1 .
Filtered & deduped bam (70M) ./align/rep1/RBC_I_rep1.sort.nodup.bam
Bam ./Chickseq/RBC_I_rep1.sort.bam
Tag-align ./align/rep1/RBC_I_rep1.sort.nodup.tagAlign.gz
Control 1 .
Filtered & deduped bam (29M) ./align/ctl1/RBC_I_contrl.sort.nodup.bam
Bam ./Chickseq/RBC_I_contrl.sort.bam
Tag-align ./align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz
Pseudo-replicates .
Replicate 1 .
Pseudo-replicate 1 .
Tag-align ./align/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign.gz
Pseudo-replicate 2 .
Tag-align ./align/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign.gz
Signal tracks .
MACS2 .
Replicate 1 .
P-value ./signal/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bw
Peaks .
MACS2 .
Replicate 1 .
Narrow peak ./peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
Pseudo-replicates .
Replicate 1 .
Pseudo-replicate 1 .
Narrow peak ./peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
Pseudo-replicate 2 .
Narrow peak ./peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
Naive overlap .
Pseudo-replicates .
Replicate 1 .
Overlapping peak ./peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
Optimal set .
Overlapping peak ./peak/macs2/overlap/optimal_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
Conservative set .
Overlapping peak ./peak/macs2/overlap/conservative_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
QC and logs .
Fingerprint JSD Plot ./qc/rbc_h5_jsd.png
Replicate 1 .
Filtered flagstat log ./qc/rep1/RBC_I_rep1.sort.nodup.flagstat.qc
JS Distance ./qc/rep1/RBC_I_rep1.sort.nodup.jsd.qc
Dedup. log ./qc/rep1/RBC_I_rep1.sort.dup.qc
PBC log ./qc/rep1/RBC_I_rep1.sort.nodup.pbc.qc
Cross-corr. log ./qc/rep1/RBC_I_rep1.sort.no_chrM.15M.R1.cc.qc
Cross-corr. plot ./qc/rep1/RBC_I_rep1.sort.no_chrM.15M.R1.cc.plot.pdf
Control 1 .
Filtered flagstat log ./qc/ctl1/RBC_I_contrl.sort.nodup.flagstat.qc
Dedup. log ./qc/ctl1/RBC_I_contrl.sort.dup.qc
PBC log ./qc/ctl1/RBC_I_contrl.sort.nodup.pbc.qc
Naive overlap .
Overlap QC log ./qc/rbc_h5_peak_overlap_final.qc
Pseudo-replicates .
Replicate 1 .
FRiP ./peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.FRiP.qc

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



Workflow diagram (g./b. peak : gapped/broad peak from MACS2, n. peak : narrow peak from MACS2, r. peak : relaxed peak from SPP)


Flagstat (filtered) QC
 rep1
ctl1
Total7004060029914360
Total(QC-failed)00
Dupes00
Dupes(QC-failed)00
Mapped7004060029914360
Mapped(QC-failed)00
% Mapped100.00100.00
Paired7004060029914360
Paired(QC-failed)00
Read13502030014957180
Read1(QC-failed)00
Read23502030014957180
Read2(QC-failed)00
Properly Paired7004060029914360
Properly Paired(QC-failed)00
% Properly Paired100.00100.00
With itself7004060029914360
With itself(QC-failed)00
Singletons00
Singletons(QC-failed)00
% Singleton0.000.00
Diff. Chroms00
Diff. Chroms (QC-failed)00
Dup. QC
 rep1
ctl1
Unpaired Reads00
Paired Reads4108005837203018
Unmapped Reads00
Unpaired Dupes00
Paired Dupes605975822245838
Paired Opt. Dupes36910729456156
% Dupes/1000.1475110.597958
Fingerprint JS metric
% genome enriched0.362227641794
AUC0.498016876312
CHANCE divergence0.0160838769282
Elbow Point0.0
JS Distance0.526000567925
Synthetic AUC0.502861732435
Synthetic Elbow Point0.0216310585572
Synthetic JS Distance0.20386149916
Synthetic X-intercept33.9495186635
X-intercept6.28944447445
diff. enrichment0.0534432207761
Fingerprint plot

Library Complexity QC
 rep1
ctl1
Total Read Pairs4107999137201150
Distinct Read Pairs3507836115104741
One Read Pair299442685126606
Two Read Pairs43905593990386
NRF = Distinct/Total0.8539040.406029
PBC1 = OnePair/Distinct0.8536390.339404
PBC2 = OnePair/TwoPair6.8201491.284739

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

Enrichment QC (strand cross-correlation measures)
Reads15000000
Est. Fragment Len.200
Corr. Est. Fragment Len.0.230947039418322
Phantom Peak155
Corr. Phantom Peak0.2316585
Argmin. Corr.1500
Min. Corr.0.2273701
NSC1.015732
RSC0.8340871

NOTE: One end of each read-pair is randomly selected and the reads are then randomly subsampled to a max of 15M

  • 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


rep1
 
Number of peaks
rep115698
rep1-pr144524
rep1-pr244350

  • ppr1: Raw peaks called on the first pooled pseudoreplicates
  • ppr2: Raw peaks called on the second pooled pseudoreplicates
  • repi: Raw peaks called on true replicate i
  • repi-pr1 : Raw peaks called on the first pseudoreplicate from replicate i
  • repi-pr2 : Raw peaks called on the second pseudoreplicates from replicate i
  • overlap : Overlapped peaks (filtered if blacklist exists)


Enrichment QC (Fraction of reads in raw peaks)
Fraction of Reads in Peak0.017192
Enrichment QC (Fraction of reads in overlapping peaks)
Fraction of Reads in Peak0.00764244

  • ppr: Overlapping peaks comparing pooled pseudo replicates
  • rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
  • rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
  • repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)


Reproducibility QC and Peak Detection Statistics (Overlapping peaks)
Nt0
N15904
N20
Np0
N optimal5904
N conservative5904
Optimal Setself_pseudo_rep_rep1
Conservative Setself_pseudo_rep_rep1
Rescue Ratio0.0
Self Consistency Ratio1.0
Reproducibility Testpass

  • N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
  • N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
  • Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
  • Np: Pooled-pseudoreplicate consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
  • Self-consistency Ratio: max(N1,N2) / min (N1,N2)
  • Rescue Ratio: max(Np,Nt) / min (Np,Nt)
  • Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'