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
11500231
21774126
15235088
Distinct Fragments
10287792
18339333
13676552
Positions with Two Read
959053
2432435
1246969
NRF = Distinct/Total
0.894573
0.842253
0.897701
PBC1 = OneRead/Distinct
0.895976
0.843717
0.89867
PBC2 = OneRead/TwoRead
9.611167
6.361199
9.856462
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
27958
24958
Top 300000 raw peaks from spp with FDR 0.01
Peak calling statistics
Peak region size
rep1
rep2
idr_opt
overlap_opt
Min size
208.0
130.0
130.0
130.0
25 percentile
496.0
520.0
510.0
510.0
50 percentile (median)
496.0
520.0
510.0
510.0
75 percentile
496.0
520.0
510.0
510.0
Max size
496.0
520.0
510.0
510.0
Mean
495.98969883396524
519.9217886048561
504.81031613976705
509.69582018927446
rep1rep2idr_optoverlap_opt
Enrichment / Signal-to-noise ratio
Strand cross-correlation measures (trimmed/filtered SE BAM)
rep1
rep2
Number of Subsampled Reads
11500231
15000000
Estimated Fragment Length
165
185
Cross-correlation at Estimated Fragment Length
0.796504717441359
0.835326316491932
Phantom Peak
50
50
Cross-correlation at Phantom Peak
0.7961479
0.8349185
Argmin of Cross-correlation
1500
1500
Minimum of Cross-correlation
0.7920701
0.8306918
NSC (Normalized Strand Cross-correlation coeff.)
1.005599
1.005579
RSC (Relative Strand Cross-correlation coeff.)
1.087503
1.096487
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
0.4071735158527799
0.4121266793612201
Synthetic AUC
0.4972080772976336
0.4979075521670127
X-intercept
0.029059716449672014
0.028508745663101326
Synthetic X-intercept
0.0
0.0
Elbow Point
0.44256928058386935
0.4322685224001565
Synthetic Elbow Point
0.5033449262220695
0.5003241422339884
JS Distance
0.0369523550918036
0.03272069125625339
Synthetic JS Distance
0.13807466085581047
0.13454981306676309
% Genome Enriched
40.508530065837014
38.08286121524991
Diff. Enrichment
7.117070847126938
6.290449730168568
CHANCE Divergence
0.060491709997914575
0.05364263670213265
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
0.1862659424342959
0.17271450467722332
0.20467126923182155
0.18162888500043478
0.20779520411557034
0.17629295155097088
0.19170137374905608
0.18151193162513402
0.17857374131644
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
0.0880252601988824
0.07211561457474795
0.07677318338206734
0.08961567607223976
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
0.005860042077303709
0.002462305975402166
0.005468383766156923
0.0071181603665210254
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
