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Report generated at 2020-05-14 12:22:53

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	116584020	153902130
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	108771418	147991110
Mapped(QC-failed)	0	0
% Mapped	93.3000	96.1600
Paired	116584020	153902130
Paired(QC-failed)	0	0
Read1	58292010	76951065
Read1(QC-failed)	0	0
Read2	58292010	76951065
Read2(QC-failed)	0	0
Properly Paired	101930094	138621783
Properly Paired(QC-failed)	0	0
% Properly Paired	87.4300	90.0700
With itself	106253143	144978594
With itself(QC-failed)	0	0
Singletons	2518275	3012516
Singletons(QC-failed)	0	0
% Singleton	2.1600	1.9600
Diff. Chroms	3040466	4251163
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	43585280	58423843
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	593290	818600
Paired Opt. Dupes	3116	6310
% Dupes/100	0.0136	0.0140

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43585199	58422690
Distinct Read Pairs	42991911	57604109
One Read Pair	42405637	56795332
Two Read Pairs	579356	799080
NRF = Distinct/Total	0.9864	0.9860
PBC1 = OnePair/Distinct	0.9864	0.9860
PBC2 = OnePair/TwoPair	73.1944	71.0759

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	85983980	115210486
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	85983980	115210486
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	85983980	115210486
Paired(QC-failed)	0	0
Read1	42991990	57605243
Read1(QC-failed)	0	0
Read2	42991990	57605243
Read2(QC-failed)	0	0
Properly Paired	85983980	115210486
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	85983980	115210486
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	194554
Np	0
N optimal	194554
N conservative	194554
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.	265
Corr. Est. Fragment Len.	0.2038
Phantom Peak	50
Corr. Phantom Peak	0.1924
Argmin. Corr.	1500
Min. Corr.	0.1824
NSC	1.1175
RSC	2.1322

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	0.2760

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	0.1297
AUC	0.4956
CHANCE divergence	0.3758
Elbow Point	0.0000
JS Distance	0.7124
Synthetic AUC	0.5005
Synthetic Elbow Point	0.0783
Synthetic JS Distance	0.4514