Title: 4-22_K27

Report generated at Wed Jul 8 05:27:28 +07 2020

Command line arguments

-type histone -out_dir /mnt/scratch/ws/psbelokopytova/202008151203data_Polya/CNTN6_new_father/4/4-22/H3K27me3/aquas_pipeline -title 4-22_K27 -se -species hg38 -system local -nth 11 -fastq1:1 /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_20_AACTCGGA-TGCAAGAC_L00M_R1_001.fastq.gz -fastq2:1 /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_21_GTCGAGAA-CTTACAGC_L00M_R1_001.fastq.gz -ctl_fastq1:1 /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_6_CTCGACTT-GAGTGTGT_L00M_R1_001.fastq.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
Total375559173877303040829421
Total(QC-failed)000
Dupes000
Dupes(QC-failed)000
Mapped363711273747821239793431
Mapped(QC-failed)000
% Mapped96.8596.6697.46
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
Total264539392723983831679419
Total(QC-failed)000
Dupes000
Dupes(QC-failed)000
Mapped264539392723983831679419
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 Reads330230623403900536001608
Paired Reads000
Unmapped Reads000
Unpaired Dupes656912367991674322189
Paired Dupes000
Paired Opt. Dupes000
% Dupes/1000.1989250.1997460.120055
Fingerprint JS metric
 rep1
rep2
% genome enriched0.2365342147750.237062096426
AUC0.4931398458480.493233512123
CHANCE divergence0.1219510732220.120773487732
Elbow Point7.77663786966e-1826.01428633778e-187
JS Distance0.6840212245290.681110249192
Synthetic AUC0.5115844080460.496175306075
Synthetic Elbow Point0.270668831890.269861194493
Synthetic JS Distance0.3702542289790.36983561152
Synthetic X-intercept24.630330123824.3402322383
X-intercept30.864040258830.7825872536
diff. enrichment0.2661443972910.265687571321
Fingerprint plot

Library Complexity QC
 rep1
rep2
ctl1
Total Reads330146273403096535909401
Distinct Reads264760502726262031665228
One Read212001782180248527869026
Two Reads427014744172453413065
NRF = Distinct/Total0.8019490.8011120.881809
PBC1 = OneRead/Distinct0.8007300.7997210.880114
PBC2 = OneRead/TwoReads4.9647424.9357658.165396

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.175255
Corr. Est. Fragment Len.0.2128003099294270.212517308481541
Phantom Peak100100
Corr. Phantom Peak0.21843420.2185407
Argmin. Corr.15001500
Min. Corr.0.19749030.1977804
NSC1.0775231.074512
RSC0.7310010.7098585

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
rep160656
rep1-pr148088
rep1-pr248063
rep242078
rep2-pr135318
rep2-pr235303
pooled31546
ppr147468
ppr247492

  • 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 Peak0.2362720.2449950.244392
Enrichment QC (Fraction of reads in overlapping peaks)
 rep1-pr
rep1-rep2
rep2-pr
Fraction of Reads in Peak0.2260330.2325430.229432

  • 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)
Nt24057
N118724
N216405
Np23965
N optimal24057
N conservative24057
Optimal Setrep1-rep2
Conservative Setrep1-rep2
Rescue Ratio1.0038389317755059
Self Consistency Ratio1.1413593416641268
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'