Title: 14-10_CTCF

Report generated at Thu Jul 9 18:01:18 +07 2020

Command line arguments

-type TF -out_dir /mnt/scratch/ws/psbelokopytova/202008151203data_Polya/CNTN6_new_father/14-10/CTCF/aquas_pipeline -title 14-10_CTCF -se -species hg38 -system local -nth 11 -fastq1:1 /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_24_GCACACAA-GAGCAATC_L00M_R1_001.fastq.gz -fastq2:1 /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_25_CTCCTAGT-CCTCATCT_L00M_R1_001.fastq.gz -ctl_fastq1:1 /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_7_CTAGCTCA-AACTGAGG_L00M_R1_001.fastq.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
Total409438784376183841393810
Total(QC-failed)000
Dupes000
Dupes(QC-failed)000
Mapped399220314261443740233769
Mapped(QC-failed)000
% Mapped97.5097.3897.20
Paired000
Paired(QC-failed)000
Read1000
Read1(QC-failed)000
Read2000
Read2(QC-failed)000
Properly Paired000
Properly Paired(QC-failed)000
% Properly Paired-nan-nan-nan
With itself000
With itself(QC-failed)000
Singletons000
Singletons(QC-failed)000
% Singleton-nan-nan-nan
Diff. Chroms000
Diff. Chroms (QC-failed)000
Flagstat (filtered) QC
 rep1
rep2
ctl1
Total306343003226641832012967
Total(QC-failed)000
Dupes000
Dupes(QC-failed)000
Mapped306343003226641832012967
Mapped(QC-failed)000
% Mapped100.00100.00100.00
Paired000
Paired(QC-failed)000
Read1000
Read1(QC-failed)000
Read2000
Read2(QC-failed)000
Properly Paired000
Properly Paired(QC-failed)000
% Properly PairedN/AN/AN/A
With itself000
With itself(QC-failed)000
Singletons000
Singletons(QC-failed)000
% SingletonN/AN/AN/A
Diff. Chroms000
Diff. Chroms (QC-failed)000
Dup. QC
 rep1
rep2
ctl1
Unpaired Reads366011733916537936454714
Paired Reads000
Unmapped Reads000
Unpaired Dupes596687368989614441747
Paired Dupes000
Paired Opt. Dupes000
% Dupes/1000.1630240.1761490.121843
Fingerprint JS metric
 rep1
rep2
% genome enriched0.2196235410540.213059954792
AUC0.493634935690.493800146997
CHANCE divergence0.1186002527110.117960477912
Elbow Point1.76212344744e-2115.79320102595e-223
JS Distance0.7247608841690.752423147052
Synthetic AUC0.503388821880.494654141017
Synthetic Elbow Point0.2988509886810.31325684587
Synthetic JS Distance0.4002123273340.413176979613
Synthetic X-intercept19.301805764418.4714980327
X-intercept34.174470300635.5339044965
diff. enrichment0.2997828461780.312404487521
Fingerprint plot

Library Complexity QC
 rep1
rep2
ctl1
Total Reads365901013915359136343630
Distinct Reads306466193228286531997832
One Read257433322672416128112739
Two Reads408584745514553490896
NRF = Distinct/Total0.8375660.8245190.880425
PBC1 = OneRead/Distinct0.8400060.8278130.878583
PBC2 = OneRead/TwoReads6.3006115.8715648.053159

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.240245
Corr. Est. Fragment Len.0.2604608061198050.2726224000481
Phantom Peak105105
Corr. Phantom Peak0.21353260.2170869
Argmin. Corr.15001500
Min. Corr.0.14159430.1391912
NSC1.8394861.958617
RSC1.6523391.712948

NOTE: Reads from replicates are 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
rep1300000
rep1-pr1300000
rep1-pr2300000
rep2300000
rep2-pr1300000
rep2-pr2300000
pooled300000
ppr1300000
ppr2300000

  • 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 Peak0.3475640.3423950.359781
Enrichment QC (Fraction of reads in overlapping peaks)
 rep1-pr
rep1-rep2
rep2-pr
Fraction of Reads in Peak0.2926780.313950.313715

  • 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)
Nt197492
N1165448
N2175484
Np197287
N optimal197492
N conservative197492
Optimal Setrep1-rep2
Conservative Setrep1-rep2
Rescue Ratio1.001039095328126
Self Consistency Ratio1.0606595425753107
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'


Enrichment QC (Fraction of reads in IDR peaks)
 rep1-pr
rep1-rep2
rep2-pr
Fraction of Reads in Peak0.2324890.254840.251354

  • 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)
Nt82324
N167396
N272489
Np84021
N optimal84021
N conservative82324
Optimal Setpooled_pseudo_rep
Conservative Setrep1-rep2
Rescue Ratio1.0206136728050144
Self Consistency Ratio1.0755682829841533
Reproducibility Testpass

  • 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