Title: 14-10_K9

Report generated at Wed Jul 8 04:36:19 +07 2020

Command line arguments

-type histone -out_dir /mnt/scratch/ws/psbelokopytova/202008151203data_Polya/CNTN6_new_father/14-10/H3K9me3/aquas_pipeline -title 14-10_K9 -se -species hg38 -system local -nth 11 -fastq1:1 /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_16_ATCTGACC-GTACGATC_L00M_R1_001.fastq.gz -fastq2:1 /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_17_CGCTACAT-AACCTACG_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
Expand all   Collapse all
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
Total462630334670480241393810
Total(QC-failed)000
Dupes000
Dupes(QC-failed)000
Mapped406740674104278640233769
Mapped(QC-failed)000
% Mapped87.9287.8897.20
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
Total203616372024821732012967
Total(QC-failed)000
Dupes000
Dupes(QC-failed)000
Mapped203616372024821732012967
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 Reads241065472414397436454714
Paired Reads000
Unmapped Reads000
Unpaired Dupes374491038957574441747
Paired Dupes000
Paired Opt. Dupes000
% Dupes/1000.1553480.1613550.121843
Fingerprint JS metric
 rep1
rep2
% genome enriched0.1307006339430.124383077945
AUC0.4921860268060.492163216468
CHANCE divergence0.2844130242680.302046887683
Elbow Point7.89158686391e-1405.24343360211e-139
JS Distance0.7983761650950.803376425004
Synthetic AUC0.5128172559010.510631904555
Synthetic Elbow Point0.3620761991940.370150090859
Synthetic JS Distance0.4806318397640.488125008123
Synthetic X-intercept18.997188978218.6031261121
X-intercept55.284274071756.7617809959
diff. enrichment0.4837134163450.497379100513
Fingerprint plot

Library Complexity QC
 rep1
rep2
ctl1
Total Reads241056562414319736343630
Distinct Reads203783892026563431997832
One Read174841891726638128112739
Two Reads251307425890443490896
NRF = Distinct/Total0.8453780.8393930.880425
PBC1 = OneRead/Distinct0.8579770.8520030.878583
PBC2 = OneRead/TwoReads6.9572926.6690188.053159

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.225215
Corr. Est. Fragment Len.0.248661897712250.249551752787478
Phantom Peak100100
Corr. Phantom Peak0.3253390.3272238
Argmin. Corr.15001500
Min. Corr.0.23277930.2333001
NSC1.068231.06966
RSC0.17159320.1730306

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
rep1175200
rep1-pr1167190
rep1-pr2168134
rep2180457
rep2-pr1197970
rep2-pr2197452
pooled155822
ppr1177232
ppr2177254

  • 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 Peak0.5364320.5260450.539706
Enrichment QC (Fraction of reads in overlapping peaks)
 rep1-pr
rep1-rep2
rep2-pr
Fraction of Reads in Peak0.4669740.5133650.494101

  • 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)
Nt109479
N182111
N2103052
Np108844
N optimal109479
N conservative109479
Optimal Setrep1-rep2
Conservative Setrep1-rep2
Rescue Ratio1.0058340377053399
Self Consistency Ratio1.2550328214246569
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'