Title: ctcf_U87

Report generated at Fri Sep 29 12:24:41 +07 2023

Command line arguments

-type TF -out_dir /mnt/scratch/ws/psbelokopytova/202310291122data/U87_chipseq/aquas_pipeline/ -title ctcf_U87 -pe -species hg38 -system local -nth 23 -fastq1_1:1 /mnt/scratch/ws/psbelokopytova/202310291122data/U87_chipseq/raw/chip_U87-dax_1/cutadapt_chip_U87-dax_1_1.fq.gz -fastq1_2:1 /mnt/scratch/ws/psbelokopytova/202310291122data/U87_chipseq/raw/chip_U87-dax_1/cutadapt_chip_U87-dax_1_2.fq.gz -fastq2_1:1 /mnt/scratch/ws/psbelokopytova/202310291122data/U87_chipseq/raw/chip_U87-dax_2/cutadapt_chip_U87-dax_2_1.fq.gz -fastq2_2:1 /mnt/scratch/ws/psbelokopytova/202310291122data/U87_chipseq/raw/chip_U87-dax_2/cutadapt_chip_U87-dax_2_2.fq.gz -ctl_fastq1_1:1 /mnt/scratch/ws/psbelokopytova/202310291122data/U87_chipseq/raw/input_U87-dax_1/cutadapt_input_U87-dax_1_1.fq.gz -ctl_fastq1_2:1 /mnt/scratch/ws/psbelokopytova/202310291122data/U87_chipseq/raw/input_U87-dax_1/cutadapt_input_U87-dax_1_2.fq.gz -ctl_fastq2_1:1 /mnt/scratch/ws/psbelokopytova/202310291122data/U87_chipseq/raw/input_U87-dax_2/cutadapt_input_U87-dax_2_1.fq.gz -ctl_fastq2_2:1 /mnt/scratch/ws/psbelokopytova/202310291122data/U87_chipseq/raw/input_U87-dax_2/cutadapt_input_U87-dax_2_2.fq.gz

Pipeline version

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


Directories and files
Expand all   Collapse all
FilesPath

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 (raw) QC
 rep1
rep2
ctl1
ctl2
Total6201952239491312291588305692860
Total(QC-failed)0000
Dupes0000
Dupes(QC-failed)0000
Mapped5585713235962389249810765089984
Mapped(QC-failed)0000
% Mapped90.0691.0685.6789.41
Paired6201952239491312291588305692860
Paired(QC-failed)0000
Read13100976119745656145794152846430
Read1(QC-failed)0000
Read23100976119745656145794152846430
Read2(QC-failed)0000
Properly Paired3694383726174490143851042882140
Properly Paired(QC-failed)0000
% Properly Paired59.5766.2849.3350.63
With itself5186212634414674227476454718299
With itself(QC-failed)0000
Singletons399500615477152233431371685
Singletons(QC-failed)0000
% Singleton6.443.927.666.53
Diff. Chroms3643035232392494368
Diff. Chroms (QC-failed)0000
Flagstat (filtered) QC
 rep1
rep2
ctl1
ctl2
Total2984710620516218123495602503238
Total(QC-failed)0000
Dupes0000
Dupes(QC-failed)0000
Mapped2984710620516218123495602503238
Mapped(QC-failed)0000
% Mapped100.00100.00100.00100.00
Paired2984710620516218123495602503238
Paired(QC-failed)0000
Read1149235531025810961747801251619
Read1(QC-failed)0000
Read2149235531025810961747801251619
Read2(QC-failed)0000
Properly Paired2984710620516218123495602503238
Properly Paired(QC-failed)0000
% Properly Paired100.00100.00100.00100.00
With itself2984710620516218123495602503238
With itself(QC-failed)0000
Singletons0000
Singletons(QC-failed)0000
% Singleton0.000.000.000.00
Diff. Chroms0000
Diff. Chroms (QC-failed)0000
Dup. QC
 rep1
rep2
ctl1
ctl2
Unpaired Reads0000
Paired Reads161479211141366764259751300840
Unmapped Reads0000
Unpaired Dupes0000
Paired Dupes1224368115555825119549221
Paired Opt. Dupes104453290114825071249195
% Dupes/1000.0758220.1012430.0390910.037838
Fingerprint JS metric
 rep1
rep2
% genome enriched0.2577210879580.233557523494
AUC0.4947082219490.493613033117
CHANCE divergence0.1648842904980.230101464487
Elbow Point1.09221194932e-3065.28188097601e-210
JS Distance0.5717778777430.581974308992
Synthetic AUC0.5089102361620.510752656129
Synthetic Elbow Point0.05013364487940.0512958717817
Synthetic JS Distance0.2861764468390.290892215578
Synthetic X-intercept36.892687559436.2329184785
X-intercept19.128205495924.9177044233
diff. enrichment0.1683331935550.220519168065
Fingerprint plot

Library Complexity QC
 rep1
rep2
ctl1
ctl2
Total Read Pairs161376611140696163887321294496
Distinct Read Pairs149139921025205261390481245515
One Read Pair13778360920804358969851197924
Two Read Pairs105450194394123474346254
NRF = Distinct/Total0.9241730.8987540.9609180.962162
PBC1 = OnePair/Distinct0.9238550.8981660.9605700.961790
PBC2 = OnePair/TwoPair13.0662379.75489325.12102625.898820

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)
 rep1
rep2
Reads1500000015000000
Est. Fragment Len.140155
Corr. Est. Fragment Len.0.1763262484614840.170206315186292
Phantom Peak5050
Corr. Phantom Peak0.18153910.1750358
Argmin. Corr.15001500
Min. Corr.0.16903790.1624277
NSC1.0431161.047889
RSC0.58300940.6169503

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
 
rep2
 
Number of peaks
rep158
rep1-pr1300000
rep1-pr2300000
rep2300000
rep2-pr1300000
rep2-pr2300000
pooled300000
ppr171
ppr266

  • 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)
 pooled_rep
rep1
rep2
Fraction of Reads in Peak0.1349590.0001050020.152989
Enrichment QC (Fraction of reads in overlapping peaks)
 rep1-pr
rep1-rep2
rep2-pr
Fraction of Reads in Peak0.0001050029.55851e-050.0190581

  • 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)
Nt39
N138
N229744
Np17
N optimal39
N conservative39
Optimal Setrep1-rep2
Conservative Setrep1-rep2
Rescue Ratio2.2941176470588234
Self Consistency Ratio782.7368421052631
Reproducibility Testfail

  • 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'


Enrichment QC (Fraction of reads in IDR peaks)
 rep1-pr
rep1-rep2
rep2-pr
Fraction of Reads in Peak8.88427e-067.74257e-050.000105296

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


Reproducibility QC and Peak Detection Statistics (Irreproducible Discovery Rate)
Nt26
N12
N231
Np3
N optimal26
N conservative26
Optimal Setrep1-rep2
Conservative Setrep1-rep2
Rescue Ratio8.666666666666666
Self Consistency Ratio15.5
Reproducibility Testfail

  • N1: Replicate 1 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
  • N2: Replicate 2 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
  • Nt: True Replicate consistent IDR 0.05 peaks (comparing true replicates Rep1 vs Rep2 )
  • Np: Pooled-pseudoreplicate consistent IDR 0.05 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'


true reps (rep1-rep2)
 
pooled pseudo-reps
 
rep1 pseudo-reps
 
rep2 pseudo-reps