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Report generated at 2022-01-13 18:34:15

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	29297900	61483794
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	16874325	53537979
Mapped(QC-failed)	0	0
% Mapped	57.6000	87.0800
Paired	29297900	61483794
Paired(QC-failed)	0	0
Read1	14648950	30741897
Read1(QC-failed)	0	0
Read2	14648950	30741897
Read2(QC-failed)	0	0
Properly Paired	15671119	45512545
Properly Paired(QC-failed)	0	0
% Properly Paired	53.4900	74.0200
With itself	15864157	48321091
With itself(QC-failed)	0	0
Singletons	1010168	5216888
Singletons(QC-failed)	0	0
% Singleton	3.4500	8.4800
Diff. Chroms	95461	1709831
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	5600523	7051123
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	96611	302597
Paired Opt. Dupes	827	868
% Dupes/100	0.0173	0.0429

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	5599687	7050084
Distinct Read Pairs	5503097	6747724
One Read Pair	5408036	6457557
Two Read Pairs	93560	279052
NRF = Distinct/Total	0.9828	0.9571
PBC1 = OnePair/Distinct	0.9827	0.9570
PBC2 = OnePair/TwoPair	57.8029	23.1411

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	11007824	13497052
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	11007824	13497052
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	11007824	13497052
Paired(QC-failed)	0	0
Read1	5503912	6748526
Read1(QC-failed)	0	0
Read2	5503912	6748526
Read2(QC-failed)	0	0
Properly Paired	11007824	13497052
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	11007824	13497052
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	26946
Np	0
N optimal	26946
N conservative	26946
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 (8M)

	rep1
Reads	8845310
Est. Fragment Len.	225
Corr. Est. Fragment Len.	0.1222
Phantom Peak	50
Corr. Phantom Peak	0.1347
Argmin. Corr.	1500
Min. Corr.	0.1095
NSC	1.1162
RSC	0.5054

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	0.1217

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	0.1418
AUC	0.4876
CHANCE divergence	0.4747
Elbow Point	0.0000
JS Distance	0.6476
Synthetic AUC	0.5121
Synthetic Elbow Point	0.1059
Synthetic JS Distance	0.3291