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
8755037
8993152
6773488
Distinct Fragments
4057441
5137976
5603654
Positions with Two Read
908420
1224672
783347
NRF = Distinct/Total
0.463441
0.571321
0.827292
PBC1 = OneRead/Distinct
0.482252
0.574604
0.832133
PBC2 = OneRead/TwoRead
2.153968
2.410686
5.952644
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
81412
86697
Top 300000 raw peaks from spp with FDR 0.01
Peak calling statistics
Peak region size
rep1
rep2
idr_opt
overlap_opt
Min size
90.0
90.0
90.0
90.0
25 percentile
360.0
360.0
360.0
360.0
50 percentile (median)
360.0
360.0
360.0
360.0
75 percentile
360.0
360.0
360.0
360.0
Max size
360.0
360.0
360.0
360.0
Mean
359.7976465385938
359.8158644474434
347.925877763329
359.4030364588902
rep1rep2idr_optoverlap_opt
Enrichment / Signal-to-noise ratio
Strand cross-correlation measures (trimmed/filtered SE BAM)
rep1
rep2
Number of Subsampled Reads
8755037
8993152
Estimated Fragment Length
185
185
Cross-correlation at Estimated Fragment Length
0.525841979720319
0.606875929875887
Phantom Peak
55
55
Cross-correlation at Phantom Peak
0.5145933
0.5910921
Argmin of Cross-correlation
1500
1500
Minimum of Cross-correlation
0.5038531
0.5780768
NSC (Normalized Strand Cross-correlation coeff.)
1.043641
1.049819
RSC (Relative Strand Cross-correlation coeff.)
2.047353
2.212719
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
0.36398798906147006
0.3648438416027083
Synthetic AUC
0.4954764210847813
0.49598782744885955
X-intercept
0.03235111643968153
0.031335717890763864
Synthetic X-intercept
0.0
0.0
Elbow Point
0.5603264436513652
0.5647271689930399
Synthetic Elbow Point
0.5057782657070719
0.5053633259159153
JS Distance
0.05217545368197644
0.05474458053014117
Synthetic JS Distance
0.1964025350903242
0.19798623284453654
% Genome Enriched
38.05230998182656
38.18955835150345
Diff. Enrichment
8.274564199418128
8.089879638957525
CHANCE Divergence
0.0703585764628327
0.06878819172291319
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
0.40103488283002964
0.4135793622918744
0.3471964481344646
0.3710008156067108
0.34577106507209504
0.3709671419739092
0.4291429306386866
0.4070936496817534
0.40692515391945466
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
0.24758995186805707
0.15497744760411267
0.18802416827105864
0.24916820281192914
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
0.043449338319989886
0.03451715584088645
0.03944533261913907
0.044331476082037496
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
