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Report generated at 2020-07-14 18:33:05

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	115680790	103857894
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	102444543	102353291
Mapped(QC-failed)	0	0
% Mapped	88.5600	98.5500
Paired	115680790	103857894
Paired(QC-failed)	0	0
Read1	57840395	51928947
Read1(QC-failed)	0	0
Read2	57840395	51928947
Read2(QC-failed)	0	0
Properly Paired	99779560	100340149
Properly Paired(QC-failed)	0	0
% Properly Paired	86.2500	96.6100
With itself	101990377	101801899
With itself(QC-failed)	0	0
Singletons	454166	551392
Singletons(QC-failed)	0	0
% Singleton	0.3900	0.5300
Diff. Chroms	76333	131984
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	45443489	44269160
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	9018440	406091
Paired Opt. Dupes	798	1054
% Dupes/100	0.1985	0.0092

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	45442548	44267990
Distinct Read Pairs	36424247	43861911
One Read Pair	29402260	43470849
Two Read Pairs	5778971	382881
NRF = Distinct/Total	0.8015	0.9908
PBC1 = OnePair/Distinct	0.8072	0.9911
PBC2 = OnePair/TwoPair	5.0878	113.5362

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	72850098	87726138
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	72850098	87726138
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	72850098	87726138
Paired(QC-failed)	0	0
Read1	36425049	43863069
Read1(QC-failed)	0	0
Read2	36425049	43863069
Read2(QC-failed)	0	0
Properly Paired	72850098	87726138
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	72850098	87726138
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	56334
Np	0
N optimal	56334
N conservative	56334
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.	0.2613
Phantom Peak	55
Corr. Phantom Peak	0.1828
Argmin. Corr.	1500
Min. Corr.	0.1474
NSC	1.7726
RSC	3.2161

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	0.2843

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	0.2278
AUC	0.4952
CHANCE divergence	0.1114
Elbow Point	0.0000
JS Distance	0.7127
Synthetic AUC	0.5035
Synthetic Elbow Point	0.2909
Synthetic JS Distance	0.3980