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Report generated at 2019-10-13 01:23:31

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	98650580	91343384
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	96363007	89445668
Mapped(QC-failed)	0	0
% Mapped	97.6800	97.9200
Paired	98650580	91343384
Paired(QC-failed)	0	0
Read1	49325290	45671692
Read1(QC-failed)	0	0
Read2	49325290	45671692
Read2(QC-failed)	0	0
Properly Paired	94949576	87213882
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2500	95.4800
With itself	95779138	88898595
With itself(QC-failed)	0	0
Singletons	583869	547073
Singletons(QC-failed)	0	0
% Singleton	0.5900	0.6000
Diff. Chroms	148732	153599
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	42553884	38418387
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2727803	536154
Paired Opt. Dupes	15259	12827
% Dupes/100	0.0641	0.0140

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42553524	38404064
Distinct Read Pairs	39825747	37868153
One Read Pair	37257957	37343686
Two Read Pairs	2416589	515076
NRF = Distinct/Total	0.9359	0.9860
PBC1 = OnePair/Distinct	0.9355	0.9861
PBC2 = OnePair/TwoPair	15.4176	72.5013

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	79652162	75764466
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	79652162	75764466
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	79652162	75764466
Paired(QC-failed)	0	0
Read1	39826081	37882233
Read1(QC-failed)	0	0
Read2	39826081	37882233
Read2(QC-failed)	0	0
Properly Paired	79652162	75764466
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	79652162	75764466
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	168901
Np	0
N optimal	168901
N conservative	168901
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.	0.1768
Phantom Peak	50
Corr. Phantom Peak	0.1815
Argmin. Corr.	1500
Min. Corr.	0.1708
NSC	1.0350
RSC	0.5599

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	0.2377

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	0.2567
AUC	0.4954
CHANCE divergence	0.1041
Elbow Point	0.0000
JS Distance	0.6642
Synthetic AUC	0.5053
Synthetic Elbow Point	0.1698
Synthetic JS Distance	0.3206