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Report generated at 2019-10-13 01:43:15

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	100007790	115682520
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	90860450	110134967
Mapped(QC-failed)	0	0
% Mapped	90.8500	95.2000
Paired	100007790	115682520
Paired(QC-failed)	0	0
Read1	50003895	57841260
Read1(QC-failed)	0	0
Read2	50003895	57841260
Read2(QC-failed)	0	0
Properly Paired	82044428	104877577
Properly Paired(QC-failed)	0	0
% Properly Paired	82.0400	90.6600
With itself	82953765	106096677
With itself(QC-failed)	0	0
Singletons	7906685	4038290
Singletons(QC-failed)	0	0
% Singleton	7.9100	3.4900
Diff. Chroms	532898	752647
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	33669206	44143515
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1556105	1315729
Paired Opt. Dupes	2661	4867
% Dupes/100	0.0462	0.0298

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	33668308	44113008
Distinct Read Pairs	32112236	42798457
One Read Pair	30626127	41528318
Two Read Pairs	1423055	1233455
NRF = Distinct/Total	0.9538	0.9702
PBC1 = OnePair/Distinct	0.9537	0.9703
PBC2 = OnePair/TwoPair	21.5214	33.6683

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	64226202	85655572
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	64226202	85655572
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	64226202	85655572
Paired(QC-failed)	0	0
Read1	32113101	42827786
Read1(QC-failed)	0	0
Read2	32113101	42827786
Read2(QC-failed)	0	0
Properly Paired	64226202	85655572
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	64226202	85655572
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	37772
Np	0
N optimal	37772
N conservative	37772
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.	125
Corr. Est. Fragment Len.	0.1769
Phantom Peak	50
Corr. Phantom Peak	0.1898
Argmin. Corr.	1500
Min. Corr.	0.1711
NSC	1.0342
RSC	0.3121

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	0.0444

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	0.3027
AUC	0.4949
CHANCE divergence	0.1111
Elbow Point	0.0000
JS Distance	0.5376
Synthetic AUC	0.4994
Synthetic Elbow Point	0.0693
Synthetic JS Distance	0.2390