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Report generated at 2020-07-09 20:19:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	129970138	99982538
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	128544120	98422018
Mapped(QC-failed)	0	0
% Mapped	98.9000	98.4400
Paired	129970138	99982538
Paired(QC-failed)	0	0
Read1	64985069	49991269
Read1(QC-failed)	0	0
Read2	64985069	49991269
Read2(QC-failed)	0	0
Properly Paired	125784592	95501110
Properly Paired(QC-failed)	0	0
% Properly Paired	96.7800	95.5200
With itself	127977359	97903435
With itself(QC-failed)	0	0
Singletons	566761	518583
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.5200
Diff. Chroms	78090	131000
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	57910596	42065303
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	840770	256391
Paired Opt. Dupes	2847	2694
% Dupes/100	0.0145	0.0061

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	57900447	42050526
Distinct Read Pairs	57060310	41795152
One Read Pair	56242080	41551531
Two Read Pairs	800205	239437
NRF = Distinct/Total	0.9855	0.9939
PBC1 = OnePair/Distinct	0.9857	0.9942
PBC2 = OnePair/TwoPair	70.2846	173.5385

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	114139652	83617824
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	114139652	83617824
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	114139652	83617824
Paired(QC-failed)	0	0
Read1	57069826	41808912
Read1(QC-failed)	0	0
Read2	57069826	41808912
Read2(QC-failed)	0	0
Properly Paired	114139652	83617824
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	114139652	83617824
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	234629
Np	0
N optimal	234629
N conservative	234629
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.	0.1761
Phantom Peak	50
Corr. Phantom Peak	0.1764
Argmin. Corr.	1500
Min. Corr.	0.1690
NSC	1.0423
RSC	0.9682

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	0.2727

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	0.2559
AUC	0.4962
CHANCE divergence	0.1035
Elbow Point	0.0000
JS Distance	0.6836
Synthetic AUC	0.5034
Synthetic Elbow Point	0.1792
Synthetic JS Distance	0.3194