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Report generated at 2021-12-31 17:35:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	122911284	110823572
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	121851387	109263081
Mapped(QC-failed)	0	0
% Mapped	99.1400	98.5900
Paired	122911284	110823572
Paired(QC-failed)	0	0
Read1	61455642	55411786
Read1(QC-failed)	0	0
Read2	61455642	55411786
Read2(QC-failed)	0	0
Properly Paired	114935237	99432483
Properly Paired(QC-failed)	0	0
% Properly Paired	93.5100	89.7200
With itself	121428728	108603175
With itself(QC-failed)	0	0
Singletons	422659	659906
Singletons(QC-failed)	0	0
% Singleton	0.3400	0.6000
Diff. Chroms	2891134	6017113
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	52590446	44416373
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	809399	432626
Paired Opt. Dupes	2098	1846
% Dupes/100	0.0154	0.0097

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52583577	44406721
Distinct Read Pairs	51774531	43974914
One Read Pair	50995988	43564699
Two Read Pairs	752756	402407
NRF = Distinct/Total	0.9846	0.9903
PBC1 = OnePair/Distinct	0.9850	0.9907
PBC2 = OnePair/TwoPair	67.7457	108.2603

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	103562094	87967494
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103562094	87967494
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	103562094	87967494
Paired(QC-failed)	0	0
Read1	51781047	43983747
Read1(QC-failed)	0	0
Read2	51781047	43983747
Read2(QC-failed)	0	0
Properly Paired	103562094	87967494
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	103562094	87967494
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	229928
Np	0
N optimal	229928
N conservative	229928
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.	150
Corr. Est. Fragment Len.	0.1776
Phantom Peak	55
Corr. Phantom Peak	0.1713
Argmin. Corr.	1500
Min. Corr.	0.1685
NSC	1.0535
RSC	3.3180

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	0.2015

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	0.2342
AUC	0.4960
CHANCE divergence	0.1379
Elbow Point	0.0000
JS Distance	0.6170
Synthetic AUC	0.5024
Synthetic Elbow Point	0.1792
Synthetic JS Distance	0.3444