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Report generated at 2021-02-05 19:28:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	115151304	120623008
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	113894297	118852959
Mapped(QC-failed)	0	0
% Mapped	98.9100	98.5300
Paired	115151304	120623008
Paired(QC-failed)	0	0
Read1	57575652	60311504
Read1(QC-failed)	0	0
Read2	57575652	60311504
Read2(QC-failed)	0	0
Properly Paired	110397912	116324482
Properly Paired(QC-failed)	0	0
% Properly Paired	95.8700	96.4400
With itself	113360646	118246914
With itself(QC-failed)	0	0
Singletons	533651	606045
Singletons(QC-failed)	0	0
% Singleton	0.4600	0.5000
Diff. Chroms	121964	142153
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	47911224	50494792
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	487124	383179
Paired Opt. Dupes	48526	18017
% Dupes/100	0.0102	0.0076

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	47891839	50475444
Distinct Read Pairs	47405588	50093864
One Read Pair	46929474	49738212
Two Read Pairs	468841	346479
NRF = Distinct/Total	0.9898	0.9924
PBC1 = OnePair/Distinct	0.9900	0.9929
PBC2 = OnePair/TwoPair	100.0968	143.5533

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	94848200	100223226
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	94848200	100223226
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	94848200	100223226
Paired(QC-failed)	0	0
Read1	47424100	50111613
Read1(QC-failed)	0	0
Read2	47424100	50111613
Read2(QC-failed)	0	0
Properly Paired	94848200	100223226
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	94848200	100223226
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	203174
Np	0
N optimal	203174
N conservative	203174
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.	145
Corr. Est. Fragment Len.	0.1868
Phantom Peak	50
Corr. Phantom Peak	0.1894
Argmin. Corr.	1500
Min. Corr.	0.1785
NSC	1.0466
RSC	0.7655

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	0.1661

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	0.2258
AUC	0.4957
CHANCE divergence	0.1476
Elbow Point	0.0000
JS Distance	0.6089
Synthetic AUC	0.4964
Synthetic Elbow Point	0.1517
Synthetic JS Distance	0.3577