Title: P_KO_CTCF

Report generated at Mon Nov 21 18:16:02 +07 2022

Command line arguments

-type histone -out_dir /mnt/storage/home/psbelokopytova/scratch/202211261156data_polya/P_KO_CTCF/processed_P_KO_CTCF/aquas_pipeline/ -title P_KO_CTCF -pe -species mm10 -system local -nth 23 -fastq1_1:1 /mnt/storage/home/psbelokopytova/scratch/202211261156data_polya/P_KO_CTCF//raw/rep_1_P_KO_CTCF/cutadapt_rep_1_P_KO_CTCF_R1.fastq.gz -fastq1_2:1 /mnt/storage/home/psbelokopytova/scratch/202211261156data_polya/P_KO_CTCF//raw/rep_1_P_KO_CTCF/cutadapt_rep_1_P_KO_CTCF_R2.fastq.gz -fastq2_1:1 /mnt/storage/home/psbelokopytova/scratch/202211261156data_polya/P_KO_CTCF//raw/rep_2_P_KO_CTCF/cutadapt_rep_2_P_KO_CTCF_R1.fastq.gz -fastq2_2:1 /mnt/storage/home/psbelokopytova/scratch/202211261156data_polya/P_KO_CTCF//raw/rep_2_P_KO_CTCF/cutadapt_rep_2_P_KO_CTCF_R2.fastq.gz -ctl_fastq1_1:1 /mnt/storage/home/psbelokopytova/scratch/202211261156data_polya/P_KO_CTCF//raw/rep_1_P_KO_input/cutadapt_rep_1_P_KO_input_R1.fastq.gz -ctl_fastq1_2:1 /mnt/storage/home/psbelokopytova/scratch/202211261156data_polya/P_KO_CTCF//raw/rep_1_P_KO_input/cutadapt_rep_1_P_KO_input_R2.fastq.gz -ctl_fastq2_1:1 /mnt/storage/home/psbelokopytova/scratch/202211261156data_polya/P_KO_CTCF//raw/rep_2_P_KO_input/cutadapt_rep_2_P_KO_input_R1.fastq.gz -ctl_fastq2_2:1 /mnt/storage/home/psbelokopytova/scratch/202211261156data_polya/P_KO_CTCF//raw/rep_2_P_KO_input/cutadapt_rep_2_P_KO_input_R2.fastq.gz

Pipeline version

Latest git commit SHA1: /bin/bash: git: command not found (/bin/bash: git: command not found)


Directories and files
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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
Total11627382178445568946044457439570
Total(QC-failed)0000
Dupes0000
Dupes(QC-failed)0000
Mapped3806343133179788609372754508092
Mapped(QC-failed)0000
% Mapped32.7474.6396.2494.90
Paired11627382178445568946044457439570
Paired(QC-failed)0000
Read1581369189222784473022228719785
Read1(QC-failed)0000
Read2581369189222784473022228719785
Read2(QC-failed)0000
Properly Paired3703719131049348180722651314433
Properly Paired(QC-failed)0000
% Properly Paired31.8573.4491.4589.34
With itself3750487132040988469508453177654
With itself(QC-failed)0000
Singletons5585611388013986431330438
Singletons(QC-failed)0000
% Singleton0.480.641.562.32
Diff. Chroms485614600388417255407
Diff. Chroms (QC-failed)0000
Flagstat (filtered) QC
 rep1
rep2
ctl1
ctl2
Total217750849825166748396438092210
Total(QC-failed)0000
Dupes0000
Dupes(QC-failed)0000
Mapped217750849825166748396438092210
Mapped(QC-failed)0000
% Mapped100.00100.00100.00100.00
Paired217750849825166748396438092210
Paired(QC-failed)0000
Read1108875424912583374198219046105
Read1(QC-failed)0000
Read2108875424912583374198219046105
Read2(QC-failed)0000
Properly Paired217750849825166748396438092210
Properly Paired(QC-failed)0000
% Properly Paired100.00100.00100.00100.00
With itself217750849825166748396438092210
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 Reads160183858084473408599820008273
Unmapped Reads0000
Unpaired Dupes0000
Paired Dupes5130843317189344016962168
Paired Opt. Dupes0000
% Dupes/1000.320310.5710970.0100930.048089
Fingerprint JS metric
 rep1
rep2
% genome enriched0.04154337720960.088698662907
AUC0.477539871620.485160893241
CHANCE divergence0.8302612242450.65089324096
Elbow Point2.66322564243e-164.60117788892e-38
JS Distance0.8444431114980.708820442072
Synthetic AUC0.506498843650.507496098291
Synthetic Elbow Point0.2749750756940.24661672123
Synthetic JS Distance0.3768594030210.372463787557
Synthetic X-intercept15.040438272924.1002109388
X-intercept75.530320456956.7034870255
diff. enrichment0.7239843437490.523321479562
Fingerprint plot

Library Complexity QC
 rep1
rep2
ctl1
ctl2
Total Read Pairs160155858066893407710619997939
Distinct Read Pairs108855424904433373315619036171
One Read Pair7262769258333352750918366969
Two Read Pairs251800665199189913634489
NRF = Distinct/Total0.6796840.4288920.9899070.951907
PBC1 = OnePair/Distinct0.6671930.3717540.9939040.964846
PBC2 = OnePair/TwoPair2.8843371.391814176.54141128.947656

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
Reads19389296716428
Est. Fragment Len.205190
Corr. Est. Fragment Len.0.1512458230435710.153046217956465
Phantom Peak5055
Corr. Phantom Peak0.098265730.1007917
Argmin. Corr.15001500
Min. Corr.0.037826560.05306877
NSC3.9984032.883922
RSC1.8765852.094957

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
rep1126061
rep1-pr1280512
rep1-pr2280113
rep2116650
rep2-pr1150169
rep2-pr2150168
pooled146989
ppr1173938
ppr2173715

  • 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 Peak0.407740.5385770.363895
Enrichment QC (Fraction of reads in overlapping peaks)
 rep1-pr
rep1-rep2
rep2-pr
Fraction of Reads in Peak0.4067660.2992110.271348

  • 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)
Nt42085
N158606
N242439
Np52046
N optimal52046
N conservative42085
Optimal Setpooled_pseudo_rep
Conservative Setrep1-rep2
Rescue Ratio1.2366876559344184
Self Consistency Ratio1.3809467706590637
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'