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Report generated at 2020-11-22 04:53:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	75290956	239432188
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	47014155	231429253
Mapped(QC-failed)	0	0
% Mapped	62.4400	96.6600
Paired	75290956	239432188
Paired(QC-failed)	0	0
Read1	37645478	119716094
Read1(QC-failed)	0	0
Read2	37645478	119716094
Read2(QC-failed)	0	0
Properly Paired	46435615	226374121
Properly Paired(QC-failed)	0	0
% Properly Paired	61.6700	94.5500
With itself	46572292	229579189
With itself(QC-failed)	0	0
Singletons	441863	1850064
Singletons(QC-failed)	0	0
% Singleton	0.5900	0.7700
Diff. Chroms	47483	2056124
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	20254966	93939937
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7673268	11899048
Paired Opt. Dupes	7042	28578
% Dupes/100	0.3788	0.1267

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	20254384	93919009
Distinct Read Pairs	12581316	82022723
One Read Pair	7467054	71424617
Two Read Pairs	3325100	9428354
NRF = Distinct/Total	0.6212	0.8733
PBC1 = OnePair/Distinct	0.5935	0.8708
PBC2 = OnePair/TwoPair	2.2457	7.5755

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	25163396	164081778
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	25163396	164081778
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	25163396	164081778
Paired(QC-failed)	0	0
Read1	12581698	82040889
Read1(QC-failed)	0	0
Read2	12581698	82040889
Read2(QC-failed)	0	0
Properly Paired	25163396	164081778
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	25163396	164081778
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	52612
Np	0
N optimal	52612
N conservative	52612
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.	185
Corr. Est. Fragment Len.	0.1749
Phantom Peak	50
Corr. Phantom Peak	0.1670
Argmin. Corr.	1500
Min. Corr.	0.1392
NSC	1.2570
RSC	1.2856

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	0.3252

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	0.1640
AUC	0.4901
CHANCE divergence	0.2613
Elbow Point	0.0000
JS Distance	0.7425
Synthetic AUC	0.5126
Synthetic Elbow Point	0.3518
Synthetic JS Distance	0.4250