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Report generated at 2020-05-02 07:41:13

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	47257386	53978528
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	40909403	49170795
Mapped(QC-failed)	0	0
% Mapped	86.5700	91.0900
Paired	47257386	53978528
Paired(QC-failed)	0	0
Read1	23628693	26989264
Read1(QC-failed)	0	0
Read2	23628693	26989264
Read2(QC-failed)	0	0
Properly Paired	39070942	47390286
Properly Paired(QC-failed)	0	0
% Properly Paired	82.6800	87.7900
With itself	40065070	48351213
With itself(QC-failed)	0	0
Singletons	844333	819582
Singletons(QC-failed)	0	0
% Singleton	1.7900	1.5200
Diff. Chroms	742136	552046
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	17522260	19555064
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	346510	746123
Paired Opt. Dupes	3041	2623
% Dupes/100	0.0198	0.0382

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	17522067	19555000
Distinct Read Pairs	17175558	18808880
One Read Pair	16834650	18086571
Two Read Pairs	335402	699153
NRF = Distinct/Total	0.9802	0.9618
PBC1 = OnePair/Distinct	0.9802	0.9616
PBC2 = OnePair/TwoPair	50.1925	25.8693

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	34351500	37617882
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	34351500	37617882
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	34351500	37617882
Paired(QC-failed)	0	0
Read1	17175750	18808941
Read1(QC-failed)	0	0
Read2	17175750	18808941
Read2(QC-failed)	0	0
Properly Paired	34351500	37617882
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	34351500	37617882
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	39464
Np	0
N optimal	39464
N conservative	39464
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.	230
Corr. Est. Fragment Len.	0.3960
Phantom Peak	55
Corr. Phantom Peak	0.3199
Argmin. Corr.	1500
Min. Corr.	0.1829
NSC	2.1646
RSC	1.5554

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	0.4223

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	0.0741
AUC	0.4930
CHANCE divergence	0.5487
Elbow Point	0.0000
JS Distance	0.7754
Synthetic AUC	0.5119
Synthetic Elbow Point	0.3376
Synthetic JS Distance	0.5323