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Report generated at 2020-05-19 01:15:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	111955044	197624996
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	104893864	192713678
Mapped(QC-failed)	0	0
% Mapped	93.6900	97.5100
Paired	111955044	197624996
Paired(QC-failed)	0	0
Read1	55977522	98812498
Read1(QC-failed)	0	0
Read2	55977522	98812498
Read2(QC-failed)	0	0
Properly Paired	103641921	189183779
Properly Paired(QC-failed)	0	0
% Properly Paired	92.5700	95.7300
With itself	104399743	191730743
With itself(QC-failed)	0	0
Singletons	494121	982935
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.5000
Diff. Chroms	440954	1513270
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	46596451	82282989
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	375028	411217
Paired Opt. Dupes	1006	3070
% Dupes/100	0.0080	0.0050

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	46592676	82255330
Distinct Read Pairs	46217684	81844454
One Read Pair	45845620	81439605
Two Read Pairs	369173	399981
NRF = Distinct/Total	0.9920	0.9950
PBC1 = OnePair/Distinct	0.9919	0.9951
PBC2 = OnePair/TwoPair	124.1847	203.6087

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	92442846	163743544
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	92442846	163743544
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	92442846	163743544
Paired(QC-failed)	0	0
Read1	46221423	81871772
Read1(QC-failed)	0	0
Read2	46221423	81871772
Read2(QC-failed)	0	0
Properly Paired	92442846	163743544
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	92442846	163743544
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	228533
Np	0
N optimal	228533
N conservative	228533
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.	150
Corr. Est. Fragment Len.	0.2061
Phantom Peak	50
Corr. Phantom Peak	0.2119
Argmin. Corr.	1500
Min. Corr.	0.1951
NSC	1.0560
RSC	0.6515

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	0.5471

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	0.1477
AUC	0.4958
CHANCE divergence	0.1602
Elbow Point	0.0000
JS Distance	0.7856
Synthetic AUC	0.5039
Synthetic Elbow Point	0.3648
Synthetic JS Distance	0.4971