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Report generated at 2021-02-05 18:02:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	121989136	106653906
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	121155413	104801407
Mapped(QC-failed)	0	0
% Mapped	99.3200	98.2600
Paired	121989136	106653906
Paired(QC-failed)	0	0
Read1	60994568	53326953
Read1(QC-failed)	0	0
Read2	60994568	53326953
Read2(QC-failed)	0	0
Properly Paired	118692023	102958254
Properly Paired(QC-failed)	0	0
% Properly Paired	97.3000	96.5300
With itself	120703873	104098130
With itself(QC-failed)	0	0
Singletons	451540	703277
Singletons(QC-failed)	0	0
% Singleton	0.3700	0.6600
Diff. Chroms	73812	170230
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	55333742	44220133
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	601215	314126
Paired Opt. Dupes	23139	110501
% Dupes/100	0.0109	0.0071

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	55326329	44206086
Distinct Read Pairs	54725330	43892511
One Read Pair	54135216	43597064
Two Read Pairs	580120	288605
NRF = Distinct/Total	0.9891	0.9929
PBC1 = OnePair/Distinct	0.9892	0.9933
PBC2 = OnePair/TwoPair	93.3173	151.0614

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	109465054	87812014
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	109465054	87812014
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	109465054	87812014
Paired(QC-failed)	0	0
Read1	54732527	43906007
Read1(QC-failed)	0	0
Read2	54732527	43906007
Read2(QC-failed)	0	0
Properly Paired	109465054	87812014
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	109465054	87812014
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	253839
Np	0
N optimal	253839
N conservative	253839
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.	0.1856
Phantom Peak	55
Corr. Phantom Peak	0.1805
Argmin. Corr.	1500
Min. Corr.	0.1708
NSC	1.0870
RSC	1.5299

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	0.4138

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	0.1910
AUC	0.4960
CHANCE divergence	0.1205
Elbow Point	0.0000
JS Distance	0.7476
Synthetic AUC	0.5019
Synthetic Elbow Point	0.2321
Synthetic JS Distance	0.4266