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Report generated at 2020-05-23 16:17:16

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	175837262	145469574
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	161641916	141586568
Mapped(QC-failed)	0	0
% Mapped	91.9300	97.3300
Paired	175837262	145469574
Paired(QC-failed)	0	0
Read1	87918631	72734787
Read1(QC-failed)	0	0
Read2	87918631	72734787
Read2(QC-failed)	0	0
Properly Paired	156894508	139229482
Properly Paired(QC-failed)	0	0
% Properly Paired	89.2300	95.7100
With itself	159357544	140814697
With itself(QC-failed)	0	0
Singletons	2284372	771871
Singletons(QC-failed)	0	0
% Singleton	1.3000	0.5300
Diff. Chroms	878601	836459
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	58653003	60565195
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	373026	282279
Paired Opt. Dupes	2370	2180
% Dupes/100	0.0064	0.0047

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	58649766	60530190
Distinct Read Pairs	58276761	60248362
One Read Pair	57913258	59967875
Two Read Pairs	355662	279160
NRF = Distinct/Total	0.9936	0.9953
PBC1 = OnePair/Distinct	0.9938	0.9953
PBC2 = OnePair/TwoPair	162.8323	214.8154

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	116559954	120565832
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116559954	120565832
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	116559954	120565832
Paired(QC-failed)	0	0
Read1	58279977	60282916
Read1(QC-failed)	0	0
Read2	58279977	60282916
Read2(QC-failed)	0	0
Properly Paired	116559954	120565832
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	116559954	120565832
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	135389
Np	0
N optimal	135389
N conservative	135389
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.	115
Corr. Est. Fragment Len.	0.2005
Phantom Peak	50
Corr. Phantom Peak	0.2454
Argmin. Corr.	1500
Min. Corr.	0.1889
NSC	1.0615
RSC	0.2053

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	0.1215

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	0.2899
AUC	0.4962
CHANCE divergence	0.0924
Elbow Point	0.0000
JS Distance	0.6004
Synthetic AUC	0.5021
Synthetic Elbow Point	0.0834
Synthetic JS Distance	0.2727