ENCSR000DYI

CEBPB ChIP-seq on human A549 produced by the Snyder lab

Pipeline version: v1.2.2

Report generated at 2019-07-13 14:30:44

Paired-end: []

Pipeline type: TF ChIP-Seq

Genome: hg38_google.tsv

Peak caller: SPP

Alignment

Flagstat (raw BAM)

	rep1	rep2	ctl1	ctl2
Total	30537463	23711730	24114469	28739630
Total(QC-failed)	0	0	0	0
Dupes	0	0	0	0
Dupes(QC-failed)	0	0	0	0
Mapped	30274746	23220534	23881180	27468951
Mapped(QC-failed)	0	0	0	0
% Mapped	99.1400	97.9300	99.0300	95.5800
Paired	0	0	0	0
Paired(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	0	0	0	0
Properly Paired(QC-failed)	0	0	0	0
% Properly Paired	0.0000	0.0000	0.0000	0.0000
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	0.0000	0.0000	0.0000	0.0000
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAM)

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)

	rep1	rep2	ctl1	ctl2
Unpaired Reads	23054530	17329108	18232260	20521787
Paired Reads	0	0	0	0
Unmapped Reads	0	0	0	0
Unpaired Dupes	1182695	651709	3011607	880764
Paired Dupes	0	0	0	0
Paired Opt. Dupes	0	0	0	0
% Dupes/100	0.0513	0.0376	0.1652	0.0429

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1	ctl2
Total Reads (Pairs)	22983515	17255729	18145142	20409245
Distinct Reads (Pairs)	21860128	16665253	15210785	19628350
One Read (Pair)	20831085	16136326	12643826	18877521
Two Reads (Pairs)	954716	482701	2241592	726308
NRF = Distinct/Total	0.9511	0.9658	0.8383	0.9617
PBC1 = OnePair/Distinct	0.9529	0.9683	0.8312	0.9617
PBC2 = OnePair/TwoPair	21.8191	33.4292	5.6406	25.9911

Mitochondrial reads are filtered out.

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

Flagstat (filtered/deduped BAM)

Filtered and duplicates removed

	rep1	rep2	ctl1	ctl2
Total	21871835	16677399	15220653	19641023
Total(QC-failed)	0	0	0	0
Dupes	0	0	0	0
Dupes(QC-failed)	0	0	0	0
Mapped	21871835	16677399	15220653	19641023
Mapped(QC-failed)	0	0	0	0
% Mapped	100.0000	100.0000	100.0000	100.0000
Paired	0	0	0	0
Paired(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	0	0	0	0
Properly Paired(QC-failed)	0	0	0	0
% Properly Paired	0.0000	0.0000	0.0000	0.0000
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	0.0000	0.0000	0.0000	0.0000
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0

Peak calling

IDR (Irreproducible Discovery Rate) plots

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller SPP

	overlap	IDR
Nt	123178	43744
N1	85732	28780
N2	87652	28410
Np	126008	46864
N optimal	126008	46864
N conservative	123178	43744
Optimal Set	ppr	ppr
Conservative Set	rep1-rep2	rep1-rep2
Rescue Ratio	1.0230	1.0713
Self Consistency Ratio	1.0224	1.0130
Reproducibility	pass	pass

Overlapping peaks

N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent overlapping 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'

IDR (Irreproducible Discovery Rate) peaks

N1: Replicate 1 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consistent IDR 0.05 peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent IDR 0.05 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'

Enrichment

Strand cross-correlation measures

Performed on subsampled reads (15M)

	rep1	rep2
Reads	15000000	15000000
Est. Fragment Len.	120	105
Corr. Est. Fragment Len.	0.2094	0.2278
Phantom Peak	40	40
Corr. Phantom Peak	0.1964	0.2087
Argmin. Corr.	1500	1500
Min. Corr.	0.1661	0.1639
NSC	1.2608	1.3899
RSC	1.4310	1.4268

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

Fraction of reads in overlapping peaks

	rep1-rep2	rep1-pr	rep2-pr	ppr
Fraction of Reads in Peak	0.1318	0.1033	0.1286	0.1334

ppr: Overlapping peaks comparing pooled pseudo replicates
rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)

Fraction of reads in IDR peaks

	rep1-rep2	rep1-pr	rep2-pr	ppr
Fraction of Reads in Peak	0.0848	0.0643	0.0779	0.0876

ppr: IDR peaks comparing pooled pseudo replicates
rep1-pr: IDR peaks comparing pseudoreplicates from replicate 1
rep2-pr: IDR peaks comparing pseudoreplicates from replicate 2
repi-repj: IDR peaks comparing true replicates (rep i vs. rep j)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1	rep2
% genome enriched	0.2334	0.2115
AUC	0.4875	0.4857
CHANCE divergence	0.1898	0.2383
Elbow Point	0.0000	0.0000
JS Distance	0.6190	0.6228
Synthetic AUC	0.5229	0.4964
Synthetic Elbow Point	0.1215	0.1413
Synthetic JS Distance	0.3010	0.3148