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Report generated at 2019-10-13 03:09:07

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	107572674	115682520
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	98412977	110134967
Mapped(QC-failed)	0	0
% Mapped	91.4900	95.2000
Paired	107572674	115682520
Paired(QC-failed)	0	0
Read1	53786337	57841260
Read1(QC-failed)	0	0
Read2	53786337	57841260
Read2(QC-failed)	0	0
Properly Paired	89273110	104877577
Properly Paired(QC-failed)	0	0
% Properly Paired	82.9900	90.6600
With itself	90095231	106096677
With itself(QC-failed)	0	0
Singletons	8317746	4038290
Singletons(QC-failed)	0	0
% Singleton	7.7300	3.4900
Diff. Chroms	540700	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	37146551	44143515
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1523357	1315729
Paired Opt. Dupes	2815	4867
% Dupes/100	0.0410	0.0298

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	37146225	44113008
Distinct Read Pairs	35622876	42798457
One Read Pair	34165184	41528318
Two Read Pairs	1395213	1233455
NRF = Distinct/Total	0.9590	0.9702
PBC1 = OnePair/Distinct	0.9591	0.9703
PBC2 = OnePair/TwoPair	24.4874	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	71246388	85655572
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71246388	85655572
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	71246388	85655572
Paired(QC-failed)	0	0
Read1	35623194	42827786
Read1(QC-failed)	0	0
Read2	35623194	42827786
Read2(QC-failed)	0	0
Properly Paired	71246388	85655572
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	71246388	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	159281
Np	0
N optimal	159281
N conservative	159281
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.	0.1744
Phantom Peak	50
Corr. Phantom Peak	0.1793
Argmin. Corr.	1500
Min. Corr.	0.1716
NSC	1.0165
RSC	0.3696

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	0.1147

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	0.2602
AUC	0.4952
CHANCE divergence	0.1290
Elbow Point	0.0000
JS Distance	0.5933
Synthetic AUC	0.5073
Synthetic Elbow Point	0.1236
Synthetic JS Distance	0.2984