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Report generated at 2020-05-02 02:52:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	177797116	226039766
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	175680498	215792212
Mapped(QC-failed)	0	0
% Mapped	98.8100	95.4700
Paired	177797116	226039766
Paired(QC-failed)	0	0
Read1	88898558	113019883
Read1(QC-failed)	0	0
Read2	88898558	113019883
Read2(QC-failed)	0	0
Properly Paired	173242735	149610065
Properly Paired(QC-failed)	0	0
% Properly Paired	97.4400	66.1900
With itself	174488852	208550402
With itself(QC-failed)	0	0
Singletons	1191646	7241810
Singletons(QC-failed)	0	0
% Singleton	0.6700	3.2000
Diff. Chroms	464683	32458811
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	74443663	41768222
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	43491148	7918296
Paired Opt. Dupes	26595	11778
% Dupes/100	0.5842	0.1896

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	74440832	41735683
Distinct Read Pairs	30951257	33824497
One Read Pair	12276343	27302863
Two Read Pairs	7454450	5377332
NRF = Distinct/Total	0.4158	0.8104
PBC1 = OnePair/Distinct	0.3966	0.8072
PBC2 = OnePair/TwoPair	1.6468	5.0774

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	61905030	67699852
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	61905030	67699852
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	61905030	67699852
Paired(QC-failed)	0	0
Read1	30952515	33849926
Read1(QC-failed)	0	0
Read2	30952515	33849926
Read2(QC-failed)	0	0
Properly Paired	61905030	67699852
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	61905030	67699852
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	96275
Np	0
N optimal	96275
N conservative	96275
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.	195
Corr. Est. Fragment Len.	0.1410
Phantom Peak	50
Corr. Phantom Peak	0.1452
Argmin. Corr.	1500
Min. Corr.	0.1352
NSC	1.0426
RSC	0.5807

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	0.2994

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	0.2179
AUC	0.4937
CHANCE divergence	0.1227
Elbow Point	0.0000
JS Distance	0.7286
Synthetic AUC	0.5101
Synthetic Elbow Point	0.1566
Synthetic JS Distance	0.3800