Open chromatin assays are known to have significant GC bias. Please take this
into consideration as necessary.
Library complexity quality metrics
Library complexity (filtered non-mito BAM)
rep1
rep2
ctl1
Total Fragments
10492945
14415319
11809199
Distinct Fragments
9428001
12755782
10907889
Positions with Two Read
801578
1232558
751083
NRF = Distinct/Total
0.898509
0.884877
0.923677
PBC1 = OneRead/Distinct
0.905458
0.891195
0.925599
PBC2 = OneRead/TwoRead
10.649812
9.223
13.442371
Mitochondrial reads are filtered out by default.
The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads
in a dataset; it is the ratio between the number of positions in the genome
that uniquely mapped reads map to and the total number of uniquely mappable
reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations
with EXACTLY one read pair over the genomic locations with AT LEAST one read
pair. PBC1 is the primary measure, and the PBC1 should be close to 1.
Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking,
0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is
the ratio of genomic locations with EXACTLY one read pair over the genomic
locations with EXACTLY two read pairs. The PBC2 should be significantly
greater than 1. See more details at
the ENCODE portal standard for ChIP-Seq pipeline
NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally
N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent 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'
Number of raw peaks
rep1
rep2
Number of peaks
49517
33546
Top 300000 raw peaks from spp with FDR 0.01
Peak calling statistics
Peak region size
rep1
rep2
idr_opt
overlap_opt
Min size
99.0
104.0
101.0
101.0
25 percentile
396.0
416.0
404.0
404.0
50 percentile (median)
396.0
416.0
404.0
404.0
75 percentile
396.0
416.0
404.0
404.0
Max size
487.0
509.0
540.0
540.0
Mean
395.0294646283095
414.50628987062544
381.13759536963954
400.32617505744724
rep1rep2idr_optoverlap_opt
Enrichment / Signal-to-noise ratio
Strand cross-correlation measures (trimmed/filtered SE BAM)
rep1
rep2
Number of Subsampled Reads
10492945
14415319
Estimated Fragment Length
180
185
Cross-correlation at Estimated Fragment Length
0.787442382603538
0.833381687737442
Phantom Peak
55
50
Cross-correlation at Phantom Peak
0.7808956
0.8276033
Argmin of Cross-correlation
1500
1500
Minimum of Cross-correlation
0.77066
0.8186007
NSC (Normalized Strand Cross-correlation coeff.)
1.021777
1.018056
RSC (Relative Strand Cross-correlation coeff.)
1.639619
1.641859
Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50.
Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only.
Untrimmed FASTQs are used for all the other analyses.
NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.
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
rep1rep2
Jensen-Shannon distance (filtered/deduped BAM)
rep1
rep2
AUC
0.37458801608831305
0.3861580145580315
Synthetic AUC
0.4970851552626774
0.497493409916687
X-intercept
0.029474877687042513
0.028947898971792667
Synthetic X-intercept
0.0
0.0
Elbow Point
0.5260824522076216
0.5101832648327541
Synthetic Elbow Point
0.5038573829080176
0.5042012820918591
JS Distance
0.08947178908648894
0.07405786354879682
Synthetic JS Distance
0.18157670121162178
0.1682831756677748
% Genome Enriched
37.42626789282371
36.56014643620663
Diff. Enrichment
12.068867382171044
9.982153397117377
CHANCE Divergence
0.10273468187472208
0.08512403487357136
Peak enrichment
Fraction of reads in peaks (FRiP)
FRiP for spp raw peaks
rep1
rep2
rep1-pr1
rep2-pr1
rep1-pr2
rep2-pr2
pooled
pooled-pr1
pooled-pr2
Fraction of Reads in Peaks
0.315505180678107
0.2318810693012928
0.28601538666054765
0.22786304419690262
0.28493263890711695
0.2268096842896772
0.3285898157335373
0.2762659188068413
0.2731158364269449
FRiP for overlap peaks
rep1_vs_rep2
rep1-pr1_vs_rep1-pr2
rep2-pr1_vs_rep2-pr2
pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks
0.1701021838879855
0.15246178524889015
0.12291693193945996
0.17508659150124375
FRiP for IDR peaks
rep1_vs_rep2
rep1-pr1_vs_rep1-pr2
rep2-pr1_vs_rep2-pr2
pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks
0.04833048238157707
0.03576782585944558
0.03407898760084638
0.04819177040707128
For spp raw peaks:
repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)
For overlap/IDR peaks:
repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates
