Title: melano_H3K27ac_kit30_mouse

Report generated at Fri Nov 26 15:48:18 +07 2021

Command line arguments

-type histone -out_dir /mnt/storage/home/psbelokopytova/scratch/202112281307data_Polya/melano_chipseq/processed_melano_H3K27ac_kit30/aquas_pipeline/ -title melano_H3K27ac_kit30_mouse -pe -species mm10 -system local -nth 23 -fastq1_1:1 /mnt/scratch/ws/psbelokopytova/202112281307data_Polya/melano_chipseq/raw/NR1/cutadapt_211102_M067_V350034057_L04_NR1_1.fq.gz -fastq1_2:1 /mnt/scratch/ws/psbelokopytova/202112281307data_Polya/melano_chipseq/raw/NR1/cutadapt_211102_M067_V350034057_L04_NR1_2.fq.gz -ctl_fastq1_1:1 /mnt/scratch/ws/psbelokopytova/202112281307data_Polya/melano_chipseq/raw/NR2/cutadapt_211102_M067_V350034057_L04_NR2_1.fq.gz -ctl_fastq1_2:1 /mnt/scratch/ws/psbelokopytova/202112281307data_Polya/melano_chipseq/raw/NR2/cutadapt_211102_M067_V350034057_L04_NR2_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
ctl1
Total2287097832702854
Total(QC-failed)00
Dupes00
Dupes(QC-failed)00
Mapped2020097930956203
Mapped(QC-failed)00
% Mapped88.3394.66
Paired2287097832702854
Paired(QC-failed)00
Read11143548916351427
Read1(QC-failed)00
Read21143548916351427
Read2(QC-failed)00
Properly Paired1873653125001972
Properly Paired(QC-failed)00
% Properly Paired81.9276.45
With itself2008000330670791
With itself(QC-failed)00
Singletons120976285412
Singletons(QC-failed)00
% Singleton0.530.87
Diff. Chroms1284354041
Diff. Chroms (QC-failed)00
Flagstat (filtered) QC
 rep1
ctl1
Total1635584421230842
Total(QC-failed)00
Dupes00
Dupes(QC-failed)00
Mapped1635584421230842
Mapped(QC-failed)00
% Mapped100.00100.00
Paired1635584421230842
Paired(QC-failed)00
Read1817792210615421
Read1(QC-failed)00
Read2817792210615421
Read2(QC-failed)00
Properly Paired1635584421230842
Properly Paired(QC-failed)00
% Properly Paired100.00100.00
With itself1635584421230842
With itself(QC-failed)00
Singletons00
Singletons(QC-failed)00
% Singleton0.000.00
Diff. Chroms00
Diff. Chroms (QC-failed)00
Dup. QC
 rep1
ctl1
Unpaired Reads00
Paired Reads851181410915794
Unmapped Reads00
Unpaired Dupes00
Paired Dupes333892300373
Paired Opt. Dupes274683276047
% Dupes/1000.0392270.027517
Fingerprint JS metric
% genome enriched0.221480653323
AUC0.493318898094
CHANCE divergence0.237926235769
Elbow Point8.37418354597e-192
JS Distance0.601134895848
Synthetic AUC0.511194139269
Synthetic Elbow Point0.0979543352709
Synthetic JS Distance0.311287459113
Synthetic X-intercept35.5230798146
X-intercept33.4467490692
diff. enrichment0.292277611461
Fingerprint plot

Library Complexity QC
 rep1
ctl1
Total Read Pairs851166610902021
Distinct Read Pairs817778010601955
One Read Pair785832510342603
Two Read Pairs306992247982
NRF = Distinct/Total0.9607730.972476
PBC1 = OnePair/Distinct0.9609360.975537
PBC2 = OnePair/TwoPair25.59781741.707071

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)
Reads10264848
Est. Fragment Len.220
Corr. Est. Fragment Len.0.140641013517864
Phantom Peak50
Corr. Phantom Peak0.1438921
Argmin. Corr.1500
Min. Corr.0.135135
NSC1.040745
RSC0.6287483

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
 
Number of peaks
rep1106827
rep1-pr1110104
rep1-pr2110232

  • 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)
Fraction of Reads in Peak0.143052
Enrichment QC (Fraction of reads in overlapping peaks)
Fraction of Reads in Peak0.0769708

  • 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)
Nt0
N126730
N20
Np0
N optimal26730
N conservative26730
Optimal Setself_pseudo_rep_rep1
Conservative Setself_pseudo_rep_rep1
Rescue Ratio0.0
Self Consistency Ratio1.0
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'