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Report generated at 2020-05-26 13:43:42

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	53695788	199901914
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52216336	196913276
Mapped(QC-failed)	0	0
% Mapped	97.2400	98.5000
Paired	53695788	199901914
Paired(QC-failed)	0	0
Read1	26847894	99950957
Read1(QC-failed)	0	0
Read2	26847894	99950957
Read2(QC-failed)	0	0
Properly Paired	51762018	192680093
Properly Paired(QC-failed)	0	0
% Properly Paired	96.4000	96.3900
With itself	51892604	195797647
With itself(QC-failed)	0	0
Singletons	323732	1115629
Singletons(QC-failed)	0	0
% Singleton	0.6000	0.5600
Diff. Chroms	26688	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	22929305	85640559
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2230846	851284
Paired Opt. Dupes	2291	5480
% Dupes/100	0.0973	0.0099

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22909784	85585893
Distinct Read Pairs	20680962	84745487
One Read Pair	18635333	83939401
Two Read Pairs	1880593	790418
NRF = Distinct/Total	0.9027	0.9902
PBC1 = OnePair/Distinct	0.9011	0.9905
PBC2 = OnePair/TwoPair	9.9093	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	41396918	169578550
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	41396918	169578550
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	41396918	169578550
Paired(QC-failed)	0	0
Read1	20698459	84789275
Read1(QC-failed)	0	0
Read2	20698459	84789275
Read2(QC-failed)	0	0
Properly Paired	41396918	169578550
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	41396918	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	34322
Np	0
N optimal	34322
N conservative	34322
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.	170
Corr. Est. Fragment Len.	0.1991
Phantom Peak	50
Corr. Phantom Peak	0.1860
Argmin. Corr.	1500
Min. Corr.	0.1653
NSC	1.2043
RSC	1.6360

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	0.2287

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	0.2350
AUC	0.4937
CHANCE divergence	0.1261
Elbow Point	0.0000
JS Distance	0.6643
Synthetic AUC	0.4992
Synthetic Elbow Point	0.2660
Synthetic JS Distance	0.3672