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Report generated at 2021-06-17 10:49:29

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	77145820	57670894
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	74492403	56708226
Mapped(QC-failed)	0	0
% Mapped	96.5600	98.3300
Paired	77145820	57670894
Paired(QC-failed)	0	0
Read1	38572910	28835447
Read1(QC-failed)	0	0
Read2	38572910	28835447
Read2(QC-failed)	0	0
Properly Paired	73741188	55341987
Properly Paired(QC-failed)	0	0
% Properly Paired	95.5900	95.9600
With itself	74208602	56367811
With itself(QC-failed)	0	0
Singletons	283801	340415
Singletons(QC-failed)	0	0
% Singleton	0.3700	0.5900
Diff. Chroms	34644	99100
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	33846935	23927807
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2690378	115907
Paired Opt. Dupes	54835	38918
% Dupes/100	0.0795	0.0048

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	33845698	23926524
Distinct Read Pairs	31155407	23810626
One Read Pair	28757058	23697269
Two Read Pairs	2187350	111925
NRF = Distinct/Total	0.9205	0.9952
PBC1 = OnePair/Distinct	0.9230	0.9952
PBC2 = OnePair/TwoPair	13.1470	211.7245

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	62313114	47623800
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	62313114	47623800
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	62313114	47623800
Paired(QC-failed)	0	0
Read1	31156557	23811900
Read1(QC-failed)	0	0
Read2	31156557	23811900
Read2(QC-failed)	0	0
Properly Paired	62313114	47623800
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	62313114	47623800
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	104245
Np	0
N optimal	104245
N conservative	104245
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.	145
Corr. Est. Fragment Len.	0.2513
Phantom Peak	55
Corr. Phantom Peak	0.1864
Argmin. Corr.	1500
Min. Corr.	0.1518
NSC	1.6553
RSC	2.8803

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	0.4280

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	0.1635
AUC	0.4947
CHANCE divergence	0.1482
Elbow Point	0.0000
JS Distance	0.8031
Synthetic AUC	0.5039
Synthetic Elbow Point	0.3568
Synthetic JS Distance	0.4891