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Report generated at 2021-02-05 12:16:09

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	55342088	116192420
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54943782	114414455
Mapped(QC-failed)	0	0
% Mapped	99.2800	98.4700
Paired	55342088	116192420
Paired(QC-failed)	0	0
Read1	27671044	58096210
Read1(QC-failed)	0	0
Read2	27671044	58096210
Read2(QC-failed)	0	0
Properly Paired	54601599	112395947
Properly Paired(QC-failed)	0	0
% Properly Paired	98.6600	96.7300
With itself	54739969	113797135
With itself(QC-failed)	0	0
Singletons	203813	617320
Singletons(QC-failed)	0	0
% Singleton	0.3700	0.5300
Diff. Chroms	26160	139100
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	25170613	48485442
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	350461	313079
Paired Opt. Dupes	31759	27712
% Dupes/100	0.0139	0.0065

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	25149638	48477890
Distinct Read Pairs	24799888	48165003
One Read Pair	24470966	47872397
Two Read Pairs	311955	285372
NRF = Distinct/Total	0.9861	0.9935
PBC1 = OnePair/Distinct	0.9867	0.9939
PBC2 = OnePair/TwoPair	78.4439	167.7544

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	49640304	96344726
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49640304	96344726
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	49640304	96344726
Paired(QC-failed)	0	0
Read1	24820152	48172363
Read1(QC-failed)	0	0
Read2	24820152	48172363
Read2(QC-failed)	0	0
Properly Paired	49640304	96344726
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	49640304	96344726
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	113380
Np	0
N optimal	113380
N conservative	113380
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.	150
Corr. Est. Fragment Len.	0.2357
Phantom Peak	55
Corr. Phantom Peak	0.1952
Argmin. Corr.	1500
Min. Corr.	0.1688
NSC	1.3957
RSC	2.5320

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	0.4745

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	0.1454
AUC	0.4940
CHANCE divergence	0.1835
Elbow Point	0.0000
JS Distance	0.8109
Synthetic AUC	0.5016
Synthetic Elbow Point	0.3745
Synthetic JS Distance	0.5053