CEBPB ChIP-seq on human A549 produced by the Snyder lab
Pipeline version
v1.3.0
Pipeline type
tf
Genome
hg38
Paired-end per replicate
[False, False]
Aligner
bowtie2
Peak caller
spp
Control paired-end per replicate
[False, False]
Alignment quality metrics
SAMstat (raw BAM)
rep1
rep2
ctl1
ctl2
Total Reads
30537463
23711730
24114469
28739630
Total Reads (QC-failed)
0
0
0
0
Duplicate Reads
0
0
0
0
Duplicate Reads (QC-failed)
0
0
0
0
Mapped Reads
30222340
23183896
23853627
27450059
Mapped Reads (QC-failed)
0
0
0
0
% Mapped Reads
99.0
97.8
98.9
95.5
Paired Reads
0
0
0
0
Paired Reads (QC-failed)
0
0
0
0
Read1
0
0
0
0
Read1 (QC-failed)
0
0
0
0
Read2
0
0
0
0
Read2 (QC-failed)
0
0
0
0
Properly Paired Reads
0
0
0
0
Properly Paired Reads (QC-failed)
0
0
0
0
% Properly Paired Reads
0.0
0.0
0.0
0.0
With itself
0
0
0
0
With itself (QC-failed)
0
0
0
0
Singletons
0
0
0
0
Singletons (QC-failed)
0
0
0
0
% Singleton
0.0
0.0
0.0
0.0
Diff. Chroms
0
0
0
0
Diff. Chroms (QC-failed)
0
0
0
0
Marking duplicates (filtered BAMs)
rep1
rep2
ctl1
ctl2
Unpaired Reads
24833252
18773507
19645147
22206741
Paired Reads
0
0
0
0
Unmapped Reads
0
0
0
0
Unpaired Duplicate Reads
1308437
749134
3258048
1009458
Paired Duplicate Reads
0
0
0
0
Paired Optical Duplicate Reads
0
0
0
0
% Duplicate Reads
5.2689
3.9904
16.5845
4.5457
Filtered out (samtools view -F 1804):
read unmapped (0x4)
mate unmapped (0x8, for paired-end)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)
SAMstat (filtered/deduped BAM)
rep1
rep2
ctl1
ctl2
Total Reads
23524815
18024373
16387099
21197283
Total Reads (QC-failed)
0
0
0
0
Duplicate Reads
0
0
0
0
Duplicate Reads (QC-failed)
0
0
0
0
Mapped Reads
23524815
18024373
16387099
21197283
Mapped Reads (QC-failed)
0
0
0
0
% Mapped Reads
100.0
100.0
100.0
100.0
Paired Reads
0
0
0
0
Paired Reads (QC-failed)
0
0
0
0
Read1
0
0
0
0
Read1 (QC-failed)
0
0
0
0
Read2
0
0
0
0
Read2 (QC-failed)
0
0
0
0
Properly Paired Reads
0
0
0
0
Properly Paired Reads (QC-failed)
0
0
0
0
% Properly Paired Reads
0.0
0.0
0.0
0.0
With itself
0
0
0
0
With itself (QC-failed)
0
0
0
0
Singletons
0
0
0
0
Singletons (QC-failed)
0
0
0
0
% Singleton
0.0
0.0
0.0
0.0
Diff. Chroms
0
0
0
0
Diff. Chroms (QC-failed)
0
0
0
0
Filtered and duplicates removed
Sequence quality metrics (GC bias)
rep1rep2
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
ctl2
Total Fragments
24725456
18655585
19523187
22037084
Distinct Fragments
23504249
18004007
16366190
21175789
Positions with Two Read
1024395
521014
2407053
784535
NRF = Distinct/Total
0.950609
0.965073
0.838295
0.960916
PBC1 = OneRead/Distinct
0.952894
0.968127
0.831543
0.961533
PBC2 = OneRead/TwoRead
21.863688
33.454324
5.653883
25.953244
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.
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
299681
299539
Top 300000 raw peaks from spp with FDR 0.01
Peak calling statistics
Peak region size
rep1
rep2
idr_opt
overlap_opt
Min size
65.0
62.0
64.0
64.0
25 percentile
260.0
250.0
256.0
256.0
50 percentile (median)
260.0
250.0
256.0
256.0
75 percentile
260.0
250.0
256.0
256.0
Max size
555.0
573.0
595.0
595.0
Mean
258.7149302091224
248.6829561426058
241.31618567019768
250.62229803993407
rep1rep2idr_optoverlap_opt
Enrichment / Signal-to-noise ratio
Strand cross-correlation measures
rep1
rep2
Number of Subsampled Reads
15000000
15000000
Estimated Fragment Length
125
105
Cross-correlation at Estimated Fragment Length
0.213726977759017
0.234591645399676
Phantom Peak
40
40
Cross-correlation at Phantom Peak
0.186234
0.197753
Argmin of Cross-correlation
1500
1500
Minimum of Cross-correlation
0.1595652
0.1552025
NSC (Normalized Strand Cross-correlation coeff.)
1.339433
1.511519
RSC (Relative Strand Cross-correlation coeff.)
2.030905
1.865762
Performed on subsampled reads
NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.
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
rep1
rep2
AUC
0.24612489854486916
0.22358320490160988
Synthetic AUC
0.4879294420448599
0.4862063934024705
X-intercept
0.15542439909949896
0.20150909897913893
Synthetic X-intercept
5.88431318355997e-58
3.5635064352659456e-44
Elbow Point
0.5975576108731901
0.5984453161550365
Synthetic Elbow Point
0.4987736824870932
0.4985654504847585
JS Distance
0.12000147196351121
0.14003085629763146
Synthetic JS Distance
0.29710866074047065
0.31245269780984763
% Genome Enriched
28.976179908270453
27.708800678174846
Diff. Enrichment
21.32409330020564
26.44100212998724
CHANCE Divergence
0.18217510139877083
0.22630146741719895
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
0.1778639279416225
0.21144502502250703
0.18855297316671893
0.21672164592234938
0.18860816497847763
0.21668882555242425
0.18667452658761946
0.19146722234536942
0.19175042322128766
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
0.12893763411212752
0.10122829871350741
0.12822343390252744
0.13088585509781803
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
0.0818760164458569
0.06198556715536339
0.07703918466401023
0.08468305084566273
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