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Report generated at 2020-07-14 20:56:53

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	96210480	61218190
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60449055	56551430
Mapped(QC-failed)	0	0
% Mapped	62.8300	92.3800
Paired	96210480	61218190
Paired(QC-failed)	0	0
Read1	48105240	30609095
Read1(QC-failed)	0	0
Read2	48105240	30609095
Read2(QC-failed)	0	0
Properly Paired	52087373	43003222
Properly Paired(QC-failed)	0	0
% Properly Paired	54.1400	70.2500
With itself	57172831	54252500
With itself(QC-failed)	0	0
Singletons	3276224	2298930
Singletons(QC-failed)	0	0
% Singleton	3.4100	3.7600
Diff. Chroms	3646821	7885178
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	22097252	16203032
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	979100	229718
Paired Opt. Dupes	3517	1893
% Dupes/100	0.0443	0.0142

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22072997	16200015
Distinct Read Pairs	21095010	15970340
One Read Pair	20153328	15743449
Two Read Pairs	906598	224151
NRF = Distinct/Total	0.9557	0.9858
PBC1 = OnePair/Distinct	0.9554	0.9858
PBC2 = OnePair/TwoPair	22.2296	70.2359

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	42236304	31946628
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	42236304	31946628
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	42236304	31946628
Paired(QC-failed)	0	0
Read1	21118152	15973314
Read1(QC-failed)	0	0
Read2	21118152	15973314
Read2(QC-failed)	0	0
Properly Paired	42236304	31946628
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	42236304	31946628
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	25894
Np	0
N optimal	25894
N conservative	25894
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.	265
Corr. Est. Fragment Len.	0.3248
Phantom Peak	50
Corr. Phantom Peak	0.3004
Argmin. Corr.	1500
Min. Corr.	0.1703
NSC	1.9074
RSC	1.1873

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	0.4649

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	0.1217
AUC	0.4936
CHANCE divergence	0.2404
Elbow Point	0.0000
JS Distance	0.8135
Synthetic AUC	0.4984
Synthetic Elbow Point	0.4106
Synthetic JS Distance	0.5541