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Report generated at 2020-05-04 03:15:44

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	178618844	143118944
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	160082464	139990469
Mapped(QC-failed)	0	0
% Mapped	89.6200	97.8100
Paired	178618844	143118944
Paired(QC-failed)	0	0
Read1	89309422	71559472
Read1(QC-failed)	0	0
Read2	89309422	71559472
Read2(QC-failed)	0	0
Properly Paired	155629290	137871740
Properly Paired(QC-failed)	0	0
% Properly Paired	87.1300	96.3300
With itself	157934375	139333057
With itself(QC-failed)	0	0
Singletons	2148089	657412
Singletons(QC-failed)	0	0
% Singleton	1.2000	0.4600
Diff. Chroms	996724	791791
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	61420600	60254568
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	374191	215974
Paired Opt. Dupes	1929	979
% Dupes/100	0.0061	0.0036

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	61416106	60210751
Distinct Read Pairs	61041946	59995391
One Read Pair	60674157	59781016
Two Read Pairs	362348	213430
NRF = Distinct/Total	0.9939	0.9964
PBC1 = OnePair/Distinct	0.9940	0.9964
PBC2 = OnePair/TwoPair	167.4472	280.0966

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	122092818	120077188
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	122092818	120077188
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	122092818	120077188
Paired(QC-failed)	0	0
Read1	61046409	60038594
Read1(QC-failed)	0	0
Read2	61046409	60038594
Read2(QC-failed)	0	0
Properly Paired	122092818	120077188
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	122092818	120077188
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	169665
Np	0
N optimal	169665
N conservative	169665
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.	120
Corr. Est. Fragment Len.	0.1838
Phantom Peak	50
Corr. Phantom Peak	0.2209
Argmin. Corr.	1500
Min. Corr.	0.1748
NSC	1.0520
RSC	0.1969

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	0.1116

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	0.2957
AUC	0.4963
CHANCE divergence	0.0981
Elbow Point	0.0000
JS Distance	0.5781
Synthetic AUC	0.5011
Synthetic Elbow Point	0.0938
Synthetic JS Distance	0.2587