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Report generated at 2021-10-10 13:03:13

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	179602156	123193466
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	168719630	118923949
Mapped(QC-failed)	0	0
% Mapped	93.9400	96.5300
Paired	179602156	123193466
Paired(QC-failed)	0	0
Read1	89801078	61596733
Read1(QC-failed)	0	0
Read2	89801078	61596733
Read2(QC-failed)	0	0
Properly Paired	166147304	116106964
Properly Paired(QC-failed)	0	0
% Properly Paired	92.5100	94.2500
With itself	167650835	118122229
With itself(QC-failed)	0	0
Singletons	1068795	801720
Singletons(QC-failed)	0	0
% Singleton	0.6000	0.6500
Diff. Chroms	1097296	1326630
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	71057199	48288802
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	9209592	2118238
Paired Opt. Dupes	52066	32462
% Dupes/100	0.1296	0.0439

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	71057090	48279257
Distinct Read Pairs	61847510	46161447
One Read Pair	53670937	44113515
Two Read Pairs	7250785	1980535
NRF = Distinct/Total	0.8704	0.9561
PBC1 = OnePair/Distinct	0.8678	0.9556
PBC2 = OnePair/TwoPair	7.4021	22.2735

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	123695214	92341128
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	123695214	92341128
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	123695214	92341128
Paired(QC-failed)	0	0
Read1	61847607	46170564
Read1(QC-failed)	0	0
Read2	61847607	46170564
Read2(QC-failed)	0	0
Properly Paired	123695214	92341128
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	123695214	92341128
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	144776
Np	0
N optimal	144776
N conservative	144776
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.	0.2112
Phantom Peak	50
Corr. Phantom Peak	0.2118
Argmin. Corr.	1500
Min. Corr.	0.2048
NSC	1.0312
RSC	0.9184

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	0.7050

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	0.0951
AUC	0.4955
CHANCE divergence	0.2168
Elbow Point	0.0000
JS Distance	0.8237
Synthetic AUC	0.5021
Synthetic Elbow Point	0.4953
Synthetic JS Distance	0.5999