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Report generated at 2020-04-29 09:01:31

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	165932488	172537646
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	163869495	169623970
Mapped(QC-failed)	0	0
% Mapped	98.7600	98.3100
Paired	165932488	172537646
Paired(QC-failed)	0	0
Read1	82966244	86268823
Read1(QC-failed)	0	0
Read2	82966244	86268823
Read2(QC-failed)	0	0
Properly Paired	161539140	167189082
Properly Paired(QC-failed)	0	0
% Properly Paired	97.3500	96.9000
With itself	162471795	168209596
With itself(QC-failed)	0	0
Singletons	1397700	1414374
Singletons(QC-failed)	0	0
% Singleton	0.8400	0.8200
Diff. Chroms	203142	219888
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	73940610	73240672
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6538024	4951100
Paired Opt. Dupes	2689	3081
% Dupes/100	0.0884	0.0676

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	73939782	73151550
Distinct Read Pairs	67401825	68207516
One Read Pair	61361569	63530412
Two Read Pairs	5577331	4426047
NRF = Distinct/Total	0.9116	0.9324
PBC1 = OnePair/Distinct	0.9104	0.9314
PBC2 = OnePair/TwoPair	11.0020	14.3538

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	134805172	136579144
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	134805172	136579144
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	134805172	136579144
Paired(QC-failed)	0	0
Read1	67402586	68289572
Read1(QC-failed)	0	0
Read2	67402586	68289572
Read2(QC-failed)	0	0
Properly Paired	134805172	136579144
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	134805172	136579144
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	247238
Np	0
N optimal	247238
N conservative	247238
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.	155
Corr. Est. Fragment Len.	0.1825
Phantom Peak	50
Corr. Phantom Peak	0.1833
Argmin. Corr.	1500
Min. Corr.	0.1805
NSC	1.0113
RSC	0.7277

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	0.5578

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	0.1560
AUC	0.4965
CHANCE divergence	0.1801
Elbow Point	0.0000
JS Distance	0.6980
Synthetic AUC	0.4966
Synthetic Elbow Point	0.3710
Synthetic JS Distance	0.4813