Title: ery_CAPH2_mouse

Report generated at Fri Nov 26 05:31:03 +07 2021

Command line arguments

-type TF -out_dir /mnt/scratch/ws/psbelokopytova/202112281307data_Polya/ery_chipseq_CAPH2/processed_ery_chipseq_CAPH2/aquas_pipeline/ -title ery_CAPH2_mouse -pe -species mm10 -system local -nth 23 -fastq1_1:1 /mnt/scratch/ws/psbelokopytova/202112281307data_Polya/ery_chipseq_CAPH2/raw/NR3/cutadapt_211102_M067_V350034057_L04_NR3_1.fq.gz -fastq1_2:1 /mnt/scratch/ws/psbelokopytova/202112281307data_Polya/ery_chipseq_CAPH2/raw/NR3/cutadapt_211102_M067_V350034057_L04_NR3_2.fq.gz -fastq2_1:1 /mnt/scratch/ws/psbelokopytova/202112281307data_Polya/ery_chipseq_CAPH2/raw/NR5/cutadapt_211102_M067_V350034057_L04_NR5_1.fq.gz -fastq2_2:1 /mnt/scratch/ws/psbelokopytova/202112281307data_Polya/ery_chipseq_CAPH2/raw/NR5/cutadapt_211102_M067_V350034057_L04_NR5_2.fq.gz -ctl_fastq1_1:1 /mnt/scratch/ws/psbelokopytova/202112281307data_Polya/ery_chipseq_CAPH2/raw/NR4/cutadapt_211102_M067_V350034057_L04_NR4_1.fq.gz -ctl_fastq1_2:1 /mnt/scratch/ws/psbelokopytova/202112281307data_Polya/ery_chipseq_CAPH2/raw/NR4/cutadapt_211102_M067_V350034057_L04_NR4_2.fq.gz -ctl_fastq2_1:1 /mnt/scratch/ws/psbelokopytova/202112281307data_Polya/ery_chipseq_CAPH2/raw/NR6/cutadapt_211102_M067_V350034057_L04_NR6_1.fq.gz -ctl_fastq2_2:1 /mnt/scratch/ws/psbelokopytova/202112281307data_Polya/ery_chipseq_CAPH2/raw/NR6/cutadapt_211102_M067_V350034057_L04_NR6_2.fq.gz

Pipeline version

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


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
Total14039818156088621938321019446960
Total(QC-failed)0000
Dupes0000
Dupes(QC-failed)0000
Mapped12818482142679431845469118446957
Mapped(QC-failed)0000
% Mapped91.3091.4195.2194.86
Paired14039818156088621938321019446960
Paired(QC-failed)0000
Read17019909780443196916059723480
Read1(QC-failed)0000
Read27019909780443196916059723480
Read2(QC-failed)0000
Properly Paired10795113120111291528725714097526
Properly Paired(QC-failed)0000
% Properly Paired76.8976.9578.8772.49
With itself12621176140805941827385318256150
With itself(QC-failed)0000
Singletons197306187349180838190807
Singletons(QC-failed)0000
% Singleton1.411.200.930.98
Diff. Chroms72664622345349147546
Diff. Chroms (QC-failed)0000
Flagstat (filtered) QC
 rep1
rep2
ctl1
ctl2
Total9079052103100681294855012027252
Total(QC-failed)0000
Dupes0000
Dupes(QC-failed)0000
Mapped9079052103100681294855012027252
Mapped(QC-failed)0000
% Mapped100.00100.00100.00100.00
Paired9079052103100681294855012027252
Paired(QC-failed)0000
Read14539526515503464742756013626
Read1(QC-failed)0000
Read24539526515503464742756013626
Read2(QC-failed)0000
Properly Paired9079052103100681294855012027252
Properly Paired(QC-failed)0000
% Properly Paired100.00100.00100.00100.00
With itself9079052103100681294855012027252
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 Reads4644499528259166087736128377
Unmapped Reads0000
Unpaired Dupes0000
Paired Dupes104973127557134498114751
Paired Opt. Dupes100020120576130763112015
% Dupes/1000.0226020.0241470.0203510.018725
Fingerprint JS metric
 rep1
rep2
% genome enriched0.2008121282550.213700781956
AUC0.4910213319090.49156590417
CHANCE divergence0.3563065098550.320704051314
Elbow Point1.33028767364e-1057.74288693647e-120
JS Distance0.552625896260.53105167815
Synthetic AUC0.4915519951780.49440221854
Synthetic Elbow Point0.04205159739050.0345339481209
Synthetic JS Distance0.2743734476230.272338572963
Synthetic X-intercept41.693426161832.738026209
X-intercept36.978416516834.4311119844
diff. enrichment0.34542042050.298538424687
Fingerprint plot

Library Complexity QC
 rep1
rep2
ctl1
ctl2
Total Read Pairs4643850528107066045166124212
Distinct Read Pairs4538886515352764700866009532
One Read Pair4447673503714363477235903739
Two Read Pairs86837111608117774102128
NRF = Distinct/Total0.9773970.9758490.9796460.981274
PBC1 = OnePair/Distinct0.9799040.9774170.9810880.982396
PBC2 = OnePair/TwoPair51.21864045.13245553.89749057.807252

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
Reads67347547398944
Est. Fragment Len.520160
Corr. Est. Fragment Len.0.1070653575158810.113467123485056
Phantom Peak5050
Corr. Phantom Peak0.12677310.1299499
Argmin. Corr.15001500
Min. Corr.0.10281430.1083794
NSC1.0413471.046944
RSC0.17743130.2358651

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
rep1300000
rep1-pr1212151
rep1-pr2208907
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 Peak0.172460.2916390.18628
Enrichment QC (Fraction of reads in overlapping peaks)
 rep1-pr
rep1-rep2
rep2-pr
Fraction of Reads in Peak0.05483930.02952250.0222798

  • 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)
Nt33754
N140376
N220779
Np34052
N optimal34052
N conservative33754
Optimal Setpooled_pseudo_rep
Conservative Setrep1-rep2
Rescue Ratio1.0088285832790187
Self Consistency Ratio1.9431156456037346
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 Peak0.00274880.0066030.00226107

  • 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)
Nt3801
N1813
N2551
Np2037
N optimal3801
N conservative3801
Optimal Setrep1-rep2
Conservative Setrep1-rep2
Rescue Ratio1.865979381443299
Self Consistency Ratio1.4754990925589837
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