Title: cre_K9

Report generated at Tue Jul 7 23:19:57 +07 2020

Command line arguments

-type histone -out_dir /mnt/storage/home/psbelokopytova/CNTN6_new_father/cre/aquas_pipeline -title cre_K9 -se -species hg38 -system local -nth 11 -fastq1:1 /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.fastq.gz -fastq2:1 /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.fastq.gz -ctl_fastq1:1 /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_1_TCCTGGTA-CAGATCCT_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
Total404135304230353940899254
Total(QC-failed)000
Dupes000
Dupes(QC-failed)000
Mapped351308943663867539881668
Mapped(QC-failed)000
% Mapped86.9386.6197.51
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
Total164074201699384731955110
Total(QC-failed)000
Dupes000
Dupes(QC-failed)000
Mapped164074201699384731955110
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 Reads195681412024918636120946
Paired Reads000
Unmapped Reads000
Unpaired Dupes316072132553394165836
Paired Dupes000
Paired Opt. Dupes000
% Dupes/1000.1615240.1607640.11533
Fingerprint JS metric
 rep1
rep2
% genome enriched0.102153892270.0956540147183
AUC0.4912927914270.491450156048
CHANCE divergence0.3756597677620.389676833755
Elbow Point2.29894322999e-1121.37993489251e-116
JS Distance0.8303797063430.837237292473
Synthetic AUC0.5008643332160.506719326302
Synthetic Elbow Point0.4112790013340.424145050647
Synthetic JS Distance0.5180693708210.530546299945
Synthetic X-intercept15.667684974914.4039298167
X-intercept61.192308776763.0847714933
diff. enrichment0.5399506181040.55877562942
Fingerprint plot

Library Complexity QC
 rep1
rep2
ctl1
Total Reads195674102024846136012454
Distinct Reads164242791701129631940085
One Read140582741459930628276867
Two Reads203835520810993311523
NRF = Distinct/Total0.8393690.8401280.886918
PBC1 = OneRead/Distinct0.8559450.8582120.885310
PBC2 = OneRead/TwoReads6.8968727.0151918.538931

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.245250
Corr. Est. Fragment Len.0.2725630545685360.273460929240213
Phantom Peak100100
Corr. Phantom Peak0.35982730.361253
Argmin. Corr.15001500
Min. Corr.0.25290780.2538206
NSC1.0777171.077379
RSC0.18383210.1828155

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
rep1119763
rep1-pr1139502
rep1-pr2139795
rep2115959
rep2-pr1132837
rep2-pr2133807
pooled102550
ppr1116580
ppr2117452

  • 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 Peak0.6166790.5982450.623061
Enrichment QC (Fraction of reads in overlapping peaks)
 rep1-pr
rep1-rep2
rep2-pr
Fraction of Reads in Peak0.5695930.6019720.59502

  • 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)
Nt75825
N177251
N273730
Np75647
N optimal75825
N conservative75825
Optimal Setrep1-rep2
Conservative Setrep1-rep2
Rescue Ratio1.0023530344891403
Self Consistency Ratio1.0477553234775532
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'