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
26940239
17098534
29935722
Distinct Fragments
23735514
15918329
27273976
Positions with Two Read
2287813
958907
2179576
NRF = Distinct/Total
0.881043
0.930976
0.911085
PBC1 = OneRead/Distinct
0.888077
0.935346
0.913722
PBC2 = OneRead/TwoRead
9.213585
15.527202
11.433802
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
22120
83040
Top 300000 raw peaks from spp with FDR 0.01
Peak calling statistics
Peak region size
rep1
rep2
idr_opt
overlap_opt
Min size
148.0
125.0
137.0
137.0
25 percentile
590.0
500.0
540.0
540.0
50 percentile (median)
590.0
500.0
540.0
540.0
75 percentile
590.0
500.0
540.0
540.0
Max size
590.0
500.0
540.0
540.0
Mean
589.2992766726944
499.75873073217724
505.203605514316
539.0926492486801
rep1rep2idr_optoverlap_opt
Enrichment / Signal-to-noise ratio
Strand cross-correlation measures (trimmed/filtered SE BAM)
rep1
rep2
Number of Subsampled Reads
15000000
15000000
Estimated Fragment Length
180
200
Cross-correlation at Estimated Fragment Length
0.843658090342768
0.848775413025603
Phantom Peak
50
50
Cross-correlation at Phantom Peak
0.843975
0.847484
Argmin of Cross-correlation
1500
1500
Minimum of Cross-correlation
0.8395415
0.8417665
NSC (Normalized Strand Cross-correlation coeff.)
1.004903
1.008326
RSC (Relative Strand Cross-correlation coeff.)
0.9285227
1.225868
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
0.4168381279743899
0.3967890005988288
Synthetic AUC
0.4981352556067241
0.49774086246318255
X-intercept
0.02761330584587848
0.028560184741266342
Synthetic X-intercept
0.0
0.0
Elbow Point
0.41571179723207724
0.47360525138236326
Synthetic Elbow Point
0.5001719840383758
0.4982853659335942
JS Distance
0.019604683000539906
0.04970112330761987
Synthetic JS Distance
0.13009356692986726
0.14968621159166856
% Genome Enriched
36.125627257327324
39.63866781730431
Diff. Enrichment
3.955068912853854
6.979846358911041
CHANCE Divergence
0.03383643065070674
0.059307182630276976
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
0.1569343649759041
0.45181301072148405
0.1593895208720963
0.3491790334534385
0.16063883495949716
0.3424998829691507
0.4643893809054266
0.3317868644925314
0.3431438867300081
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
0.1369057369620125
0.05944938735672052
0.1916757769944006
0.2158641039516323
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
0.00669606475892308
0.003326377391089869
0.007114523717774892
0.010111264216903242
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
