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Report generated at 2022-01-01 04:14:39

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	133115862	141252688
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	127534371	137128851
Mapped(QC-failed)	0	0
% Mapped	95.8100	97.0800
Paired	133115862	141252688
Paired(QC-failed)	0	0
Read1	66557931	70626344
Read1(QC-failed)	0	0
Read2	66557931	70626344
Read2(QC-failed)	0	0
Properly Paired	115237201	120202392
Properly Paired(QC-failed)	0	0
% Properly Paired	86.5700	85.1000
With itself	126190603	135538631
With itself(QC-failed)	0	0
Singletons	1343768	1590220
Singletons(QC-failed)	0	0
% Singleton	1.0100	1.1300
Diff. Chroms	3700677	10787220
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	51862973	53575957
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2108883	637468
Paired Opt. Dupes	1961	1319
% Dupes/100	0.0407	0.0119

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51860488	53569792
Distinct Read Pairs	49751730	52932780
One Read Pair	47727322	52328435
Two Read Pairs	1944985	584956
NRF = Distinct/Total	0.9593	0.9881
PBC1 = OnePair/Distinct	0.9593	0.9886
PBC2 = OnePair/TwoPair	24.5387	89.4570

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	99508180	105876978
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	99508180	105876978
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	99508180	105876978
Paired(QC-failed)	0	0
Read1	49754090	52938489
Read1(QC-failed)	0	0
Read2	49754090	52938489
Read2(QC-failed)	0	0
Properly Paired	99508180	105876978
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	99508180	105876978
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	200519
Np	0
N optimal	200519
N conservative	200519
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.	0.1761
Phantom Peak	55
Corr. Phantom Peak	0.1738
Argmin. Corr.	1500
Min. Corr.	0.1697
NSC	1.0376
RSC	1.5596

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	0.1924

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	0.2376
AUC	0.4959
CHANCE divergence	0.1363
Elbow Point	0.0000
JS Distance	0.6133
Synthetic AUC	0.4989
Synthetic Elbow Point	0.1649
Synthetic JS Distance	0.3389