Title: 14-10_K27

Report generated at Wed Jul 8 07:25:54 +07 2020

Command line arguments

-type histone -out_dir /mnt/scratch/ws/psbelokopytova/202008151203data_Polya/CNTN6_new_father/14-10/H3K27me3/aquas_pipeline -title 14-10_K27 -se -species hg38 -system local -nth 11 -fastq1:1 /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_22_ACAACAGC-ACCGACAA_L00M_R1_001.fastq.gz -fastq2:1 /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_23_ATGACAGG-ACATGCCA_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
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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
Total413463864484852341393810
Total(QC-failed)000
Dupes000
Dupes(QC-failed)000
Mapped401685434354163540233769
Mapped(QC-failed)000
% Mapped97.1597.0997.20
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
Total291618773203909432012967
Total(QC-failed)000
Dupes000
Dupes(QC-failed)000
Mapped291618773203909432012967
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 Reads364491873940738136454714
Paired Reads000
Unmapped Reads000
Unpaired Dupes728731073682874441747
Paired Dupes000
Paired Opt. Dupes000
% Dupes/1000.1999310.1869770.121843
Fingerprint JS metric
 rep1
rep2
% genome enriched0.1756637299890.19906059394
AUC0.4934629377060.493761775801
CHANCE divergence0.1396748344580.120869453952
Elbow Point2.04779250102e-2003.28175141294e-220
JS Distance0.8007521352480.779649563354
Synthetic AUC0.4948288443850.500825949921
Synthetic Elbow Point0.3999999826930.360028179739
Synthetic JS Distance0.4832463700060.447173781203
Synthetic X-intercept14.14322158616.3508445027
X-intercept43.137977786838.5332271537
diff. enrichment0.3854653943370.342077176182
Fingerprint plot

Library Complexity QC
 rep1
rep2
ctl1
Total Reads364427373939353136343630
Distinct Reads291860073205814131997832
One Read235177232619940228112739
Two Reads448248347326493490896
NRF = Distinct/Total0.8008730.8137920.880425
PBC1 = OneRead/Distinct0.8057880.8172460.878583
PBC2 = OneRead/TwoReads5.2465845.5358858.053159

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.295140
Corr. Est. Fragment Len.0.3164748350851540.285217762789442
Phantom Peak100100
Corr. Phantom Peak0.3195180.2890742
Argmin. Corr.15001500
Min. Corr.0.28080160.2559316
NSC1.1270411.11443
RSC0.92139950.8836401

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
rep139236
rep1-pr138190
rep1-pr238142
rep246149
rep2-pr155368
rep2-pr255381
pooled33468
ppr146877
ppr246921

  • 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 Peak0.3795340.4171230.348246
Enrichment QC (Fraction of reads in overlapping peaks)
 rep1-pr
rep1-rep2
rep2-pr
Fraction of Reads in Peak0.4056290.3747310.338706

  • 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)
Nt24566
N121034
N225629
Np27979
N optimal27979
N conservative24566
Optimal Setpooled_pseudo_rep
Conservative Setrep1-rep2
Rescue Ratio1.1389318570381828
Self Consistency Ratio1.2184558334125701
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'