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
654446
2424728
3056127
Distinct Fragments
642222
2334918
2969356
Positions with Two Read
9449
58952
63372
NRF = Distinct/Total
0.981322
0.962961
0.971608
PBC1 = OneRead/Distinct
0.98364
0.970422
0.976567
PBC2 = OneRead/TwoRead
66.855223
38.435592
45.758
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
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
Replication quality metrics
IDR (Irreproducible Discovery Rate) plots
Reproducibility QC and peak detection statistics
overlap
idr
Nt
5373
1480
N1
1461
279
N2
8737
1604
Np
8770
1889
N optimal
8770
1889
N conservative
5373
1480
Optimal Set
pooled-pr1_vs_pooled-pr2
pooled-pr1_vs_pooled-pr2
Conservative Set
rep1_vs_rep2
rep1_vs_rep2
Rescue Ratio
1.6322352503257025
1.2763513513513514
Self Consistency Ratio
5.980150581793292
5.749103942652329
Reproducibility Test
borderline
borderline
Reproducibility QC
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
18884
28640
Top 300000 raw peaks from spp with FDR 0.01
Peak calling statistics
Peak region size
rep1
rep2
idr_opt
overlap_opt
Min size
83.0
70.0
70.0
70.0
25 percentile
290.0
280.0
280.0
280.0
50 percentile (median)
290.0
280.0
280.0
280.0
75 percentile
290.0
280.0
280.0
280.0
Max size
290.0
280.0
280.0
280.0
Mean
289.93269434441856
279.8729748603352
276.2170460561143
279.18517673888255
Enrichment / Signal-to-noise ratio
Strand cross-correlation measures (trimmed/filtered SE BAM)
rep1
rep2
Number of Subsampled Reads
654446
2424728
Estimated Fragment Length
100
90
Cross-correlation at Estimated Fragment Length
0.241203528736229
0.504874775871523
Phantom Peak
40
40
Cross-correlation at Phantom Peak
0.2291813
0.4827697
Argmin of Cross-correlation
1500
1500
Minimum of Cross-correlation
0.2077775
0.4557555
NSC (Normalized Strand Cross-correlation coeff.)
1.160874
1.107775
RSC (Relative Strand Cross-correlation coeff.)
1.561687
1.818276
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
Jensen-Shannon distance (filtered/deduped BAM)
rep1
rep2
AUC
0.276882393972065
0.3314819155556074
Synthetic AUC
0.48603268804434124
0.49268250672262087
X-intercept
0.11193449293864198
0.04390010372616293
Synthetic X-intercept
4.61704772755811e-43
1.2107304524090992e-159
Elbow Point
0.6364417936647251
0.5948555812654592
Synthetic Elbow Point
0.5216727227183947
0.4963947537385754
JS Distance
0.1389196778661143
0.09291358160807613
Synthetic JS Distance
0.25930328601409364
0.23084544625484563
% Genome Enriched
35.34389212479055
35.02533312056172
Diff. Enrichment
22.5238552379176
12.543918121632263
CHANCE Divergence
0.19317837077383176
0.10670401872533422
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
0.19720013692625343
0.20386000904109344
0.13187340846710988
0.2568002397297406
0.1278651553124061
0.2537193144816352
0.17939422536342461
0.24590980248587632
0.24371753521640513
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
0.0829163654860386
0.05051091770019656
0.10062677230830043
0.1046964099269135
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
0.04656285974352796
0.01696553454677255
0.04717931117795886
0.05478609482504752
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