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Report generated at 2020-05-26 13:13:59

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	52258852	199901914
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	51548635	196913276
Mapped(QC-failed)	0	0
% Mapped	98.6400	98.5000
Paired	52258852	199901914
Paired(QC-failed)	0	0
Read1	26129426	99950957
Read1(QC-failed)	0	0
Read2	26129426	99950957
Read2(QC-failed)	0	0
Properly Paired	51201676	192680093
Properly Paired(QC-failed)	0	0
% Properly Paired	97.9800	96.3900
With itself	51305671	195797647
With itself(QC-failed)	0	0
Singletons	242964	1115629
Singletons(QC-failed)	0	0
% Singleton	0.4600	0.5600
Diff. Chroms	22305	160902
Diff. Chroms (QC-failed)	0	0

Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

	rep1	ctl1
Unpaired Reads	0	0
Paired Reads	22900376	85640559
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	640542	851284
Paired Opt. Dupes	2200	5480
% Dupes/100	0.0280	0.0099

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22885381	85585893
Distinct Read Pairs	22245449	84745487
One Read Pair	21644240	83939401
Two Read Pairs	570378	790418
NRF = Distinct/Total	0.9720	0.9902
PBC1 = OnePair/Distinct	0.9730	0.9905
PBC2 = OnePair/TwoPair	37.9472	106.1962

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	ctl1
Total	44519668	169578550
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	44519668	169578550
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	44519668	169578550
Paired(QC-failed)	0	0
Read1	22259834	84789275
Read1(QC-failed)	0	0
Read2	22259834	84789275
Read2(QC-failed)	0	0
Properly Paired	44519668	169578550
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	44519668	169578550
With itself(QC-failed)	0	0
Singletons	0	0
Singletons(QC-failed)	0	0
% Singleton	0.0000	0.0000
Diff. Chroms	0	0
Diff. Chroms (QC-failed)	0	0

Peak calling

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller MACS2

	overlap
Nt	0
N1	60294
Np	0
N optimal	60294
N conservative	60294
Optimal Set	rep1-pr
Conservative Set	rep1-pr
Rescue Ratio	0.0000
Self Consistency Ratio	1.0000
Reproducibility	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'

Enrichment

Strand cross-correlation measures

Performed on subsampled reads (15M)

	rep1
Reads	15000000
Est. Fragment Len.	175
Corr. Est. Fragment Len.	0.2356
Phantom Peak	50
Corr. Phantom Peak	0.1986
Argmin. Corr.	1500
Min. Corr.	0.1627
NSC	1.4483
RSC	2.0299

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-pr
Fraction of Reads in Peak	0.4570

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)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1
% genome enriched	0.1609
AUC	0.4939
CHANCE divergence	0.1536
Elbow Point	0.0000
JS Distance	0.8164
Synthetic AUC	0.5009
Synthetic Elbow Point	0.4102
Synthetic JS Distance	0.4961