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Report generated at 2021-10-09 23:28:39

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	115622576	116616760
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	113917735	115340967
Mapped(QC-failed)	0	0
% Mapped	98.5300	98.9100
Paired	115622576	116616760
Paired(QC-failed)	0	0
Read1	57811288	58308380
Read1(QC-failed)	0	0
Read2	57811288	58308380
Read2(QC-failed)	0	0
Properly Paired	113075328	112618961
Properly Paired(QC-failed)	0	0
% Properly Paired	97.8000	96.5700
With itself	113371827	114670631
With itself(QC-failed)	0	0
Singletons	545908	670336
Singletons(QC-failed)	0	0
% Singleton	0.4700	0.5700
Diff. Chroms	118987	1356484
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	49610418	46805405
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	9163211	2581950
Paired Opt. Dupes	41716	44282
% Dupes/100	0.1847	0.0552

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49609259	46788318
Distinct Read Pairs	40446256	44207269
One Read Pair	32722973	41662261
Two Read Pairs	6487872	2510205
NRF = Distinct/Total	0.8153	0.9448
PBC1 = OnePair/Distinct	0.8090	0.9424
PBC2 = OnePair/TwoPair	5.0437	16.5972

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	80894414	88446910
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80894414	88446910
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	80894414	88446910
Paired(QC-failed)	0	0
Read1	40447207	44223455
Read1(QC-failed)	0	0
Read2	40447207	44223455
Read2(QC-failed)	0	0
Properly Paired	80894414	88446910
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	80894414	88446910
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	106926
Np	0
N optimal	106926
N conservative	106926
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.	200
Corr. Est. Fragment Len.	0.2217
Phantom Peak	50
Corr. Phantom Peak	0.2169
Argmin. Corr.	1500
Min. Corr.	0.1888
NSC	1.1745
RSC	1.1707

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	0.5436

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	0.1376
AUC	0.4945
CHANCE divergence	0.1484
Elbow Point	0.0000
JS Distance	0.8174
Synthetic AUC	0.5098
Synthetic Elbow Point	0.4291
Synthetic JS Distance	0.5265