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Report generated at 2021-10-21 21:25:31

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	190224650	216279744
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	166115425	212268741
Mapped(QC-failed)	0	0
% Mapped	87.3300	98.1500
Paired	190224650	216279744
Paired(QC-failed)	0	0
Read1	95112325	108139872
Read1(QC-failed)	0	0
Read2	95112325	108139872
Read2(QC-failed)	0	0
Properly Paired	161277924	208007441
Properly Paired(QC-failed)	0	0
% Properly Paired	84.7800	96.1800
With itself	162933703	210903306
With itself(QC-failed)	0	0
Singletons	3181722	1365435
Singletons(QC-failed)	0	0
% Singleton	1.6700	0.6300
Diff. Chroms	937334	1643621
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	69620825	86702361
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7050844	3631684
Paired Opt. Dupes	24137	20901
% Dupes/100	0.1013	0.0419

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	69618233	86645143
Distinct Read Pairs	62567643	83016384
One Read Pair	56124383	79488299
Two Read Pairs	5883029	3431092
NRF = Distinct/Total	0.8987	0.9581
PBC1 = OnePair/Distinct	0.8970	0.9575
PBC2 = OnePair/TwoPair	9.5400	23.1671

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	125139962	166141354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	125139962	166141354
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	125139962	166141354
Paired(QC-failed)	0	0
Read1	62569981	83070677
Read1(QC-failed)	0	0
Read2	62569981	83070677
Read2(QC-failed)	0	0
Properly Paired	125139962	166141354
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	125139962	166141354
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	144242
Np	0
N optimal	144242
N conservative	144242
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.	160
Corr. Est. Fragment Len.	0.1851
Phantom Peak	50
Corr. Phantom Peak	0.1904
Argmin. Corr.	1500
Min. Corr.	0.1755
NSC	1.0550
RSC	0.6482

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	0.4208

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	0.2159
AUC	0.4955
CHANCE divergence	0.1068
Elbow Point	0.0000
JS Distance	0.7832
Synthetic AUC	0.4994
Synthetic Elbow Point	0.3031
Synthetic JS Distance	0.3971