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Report generated at 2021-10-10 15:55:14

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	146234888	202350424
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	140484402	198649849
Mapped(QC-failed)	0	0
% Mapped	96.0700	98.1700
Paired	146234888	202350424
Paired(QC-failed)	0	0
Read1	73117444	101175212
Read1(QC-failed)	0	0
Read2	73117444	101175212
Read2(QC-failed)	0	0
Properly Paired	135659283	191032553
Properly Paired(QC-failed)	0	0
% Properly Paired	92.7700	94.4100
With itself	137924233	196787032
With itself(QC-failed)	0	0
Singletons	2560169	1862817
Singletons(QC-failed)	0	0
% Singleton	1.7500	0.9200
Diff. Chroms	1553786	4083046
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	59264367	79868417
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4157663	3252613
Paired Opt. Dupes	38001	36998
% Dupes/100	0.0702	0.0407

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	59261802	79802498
Distinct Read Pairs	55104332	76553268
One Read Pair	51193660	73415319
Two Read Pairs	3676921	3032014
NRF = Distinct/Total	0.9298	0.9593
PBC1 = OnePair/Distinct	0.9290	0.9590
PBC2 = OnePair/TwoPair	13.9230	24.2134

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	110213408	153231608
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	110213408	153231608
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	110213408	153231608
Paired(QC-failed)	0	0
Read1	55106704	76615804
Read1(QC-failed)	0	0
Read2	55106704	76615804
Read2(QC-failed)	0	0
Properly Paired	110213408	153231608
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	110213408	153231608
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	134462
Np	0
N optimal	134462
N conservative	134462
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.	205
Corr. Est. Fragment Len.	0.1953
Phantom Peak	50
Corr. Phantom Peak	0.1970
Argmin. Corr.	1500
Min. Corr.	0.1814
NSC	1.0765
RSC	0.8886

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	0.5303

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	0.1742
AUC	0.4953
CHANCE divergence	0.1146
Elbow Point	0.0000
JS Distance	0.8254
Synthetic AUC	0.4979
Synthetic Elbow Point	0.3815
Synthetic JS Distance	0.4693