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Report generated at 2021-02-06 05:40:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	113584592	116192420
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	112962769	114414455
Mapped(QC-failed)	0	0
% Mapped	99.4500	98.4700
Paired	113584592	116192420
Paired(QC-failed)	0	0
Read1	56792296	58096210
Read1(QC-failed)	0	0
Read2	56792296	58096210
Read2(QC-failed)	0	0
Properly Paired	111528438	112395947
Properly Paired(QC-failed)	0	0
% Properly Paired	98.1900	96.7300
With itself	112620710	113797135
With itself(QC-failed)	0	0
Singletons	342059	617320
Singletons(QC-failed)	0	0
% Singleton	0.3000	0.5300
Diff. Chroms	48089	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	52576766	48485442
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	520563	313079
Paired Opt. Dupes	50690	27712
% Dupes/100	0.0099	0.0065

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52573388	48477890
Distinct Read Pairs	52052880	48165003
One Read Pair	51541401	47872397
Two Read Pairs	502990	285372
NRF = Distinct/Total	0.9901	0.9935
PBC1 = OnePair/Distinct	0.9902	0.9939
PBC2 = OnePair/TwoPair	102.4700	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	104112406	96344726
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	104112406	96344726
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	104112406	96344726
Paired(QC-failed)	0	0
Read1	52056203	48172363
Read1(QC-failed)	0	0
Read2	52056203	48172363
Read2(QC-failed)	0	0
Properly Paired	104112406	96344726
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	104112406	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	271849
Np	0
N optimal	271849
N conservative	271849
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.	0.1904
Phantom Peak	55
Corr. Phantom Peak	0.1827
Argmin. Corr.	1500
Min. Corr.	0.1711
NSC	1.1129
RSC	1.6632

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	0.4937

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	0.1659
AUC	0.4959
CHANCE divergence	0.1384
Elbow Point	0.0000
JS Distance	0.7590
Synthetic AUC	0.5072
Synthetic Elbow Point	0.2868
Synthetic JS Distance	0.4672