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Report generated at 2019-10-12 14:11:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	63304468	52163906
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	61790435	51011229
Mapped(QC-failed)	0	0
% Mapped	97.6100	97.7900
Paired	63304468	52163906
Paired(QC-failed)	0	0
Read1	31652234	26081953
Read1(QC-failed)	0	0
Read2	31652234	26081953
Read2(QC-failed)	0	0
Properly Paired	61013126	50327538
Properly Paired(QC-failed)	0	0
% Properly Paired	96.3800	96.4800
With itself	61259524	50605281
With itself(QC-failed)	0	0
Singletons	530911	405948
Singletons(QC-failed)	0	0
% Singleton	0.8400	0.7800
Diff. Chroms	74002	116158
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	25554865	21583364
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	678213	577632
Paired Opt. Dupes	2506	1867
% Dupes/100	0.0265	0.0268

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	25554095	21564897
Distinct Read Pairs	24875895	20987844
One Read Pair	24213609	20426550
Two Read Pairs	646855	546417
NRF = Distinct/Total	0.9735	0.9732
PBC1 = OnePair/Distinct	0.9734	0.9733
PBC2 = OnePair/TwoPair	37.4328	37.3827

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	49753304	42011464
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49753304	42011464
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	49753304	42011464
Paired(QC-failed)	0	0
Read1	24876652	21005732
Read1(QC-failed)	0	0
Read2	24876652	21005732
Read2(QC-failed)	0	0
Properly Paired	49753304	42011464
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	49753304	42011464
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	29213
Np	0
N optimal	29213
N conservative	29213
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.	135
Corr. Est. Fragment Len.	0.1730
Phantom Peak	50
Corr. Phantom Peak	0.1837
Argmin. Corr.	1500
Min. Corr.	0.1689
NSC	1.0240
RSC	0.2755

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	0.0302

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	0.3080
AUC	0.4942
CHANCE divergence	0.1126
Elbow Point	0.0000
JS Distance	0.5283
Synthetic AUC	0.4965
Synthetic Elbow Point	0.0422
Synthetic JS Distance	0.2256