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Report generated at 2019-10-12 14:05:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	63891320	82773480
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53908659	80507886
Mapped(QC-failed)	0	0
% Mapped	84.3800	97.2600
Paired	63891320	82773480
Paired(QC-failed)	0	0
Read1	31945660	41386740
Read1(QC-failed)	0	0
Read2	31945660	41386740
Read2(QC-failed)	0	0
Properly Paired	53505892	79812046
Properly Paired(QC-failed)	0	0
% Properly Paired	83.7500	96.4200
With itself	53651127	80154101
With itself(QC-failed)	0	0
Singletons	257532	353785
Singletons(QC-failed)	0	0
% Singleton	0.4000	0.4300
Diff. Chroms	43923	116542
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	24446188	35609282
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	13192019	3238943
Paired Opt. Dupes	5668	8059
% Dupes/100	0.5396	0.0910

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24444302	35576205
Distinct Read Pairs	11253245	32340103
One Read Pair	5077227	29415039
Two Read Pairs	2848585	2647904
NRF = Distinct/Total	0.4604	0.9090
PBC1 = OnePair/Distinct	0.4512	0.9096
PBC2 = OnePair/TwoPair	1.7824	11.1088

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	22508338	64740678
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	22508338	64740678
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	22508338	64740678
Paired(QC-failed)	0	0
Read1	11254169	32370339
Read1(QC-failed)	0	0
Read2	11254169	32370339
Read2(QC-failed)	0	0
Properly Paired	22508338	64740678
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	22508338	64740678
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	55370
Np	0
N optimal	55370
N conservative	55370
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.	150
Corr. Est. Fragment Len.	0.1795
Phantom Peak	50
Corr. Phantom Peak	0.1669
Argmin. Corr.	1500
Min. Corr.	0.1261
NSC	1.4230
RSC	1.3079

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	0.3415

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	0.1493
AUC	0.4914
CHANCE divergence	0.3072
Elbow Point	0.0000
JS Distance	0.7202
Synthetic AUC	0.4941
Synthetic Elbow Point	0.3138
Synthetic JS Distance	0.4447