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Report generated at 2021-10-10 07:16:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	94113970	202350424
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	88909311	198649849
Mapped(QC-failed)	0	0
% Mapped	94.4700	98.1700
Paired	94113970	202350424
Paired(QC-failed)	0	0
Read1	47056985	101175212
Read1(QC-failed)	0	0
Read2	47056985	101175212
Read2(QC-failed)	0	0
Properly Paired	86231491	191032553
Properly Paired(QC-failed)	0	0
% Properly Paired	91.6200	94.4100
With itself	87264432	196787032
With itself(QC-failed)	0	0
Singletons	1644879	1862817
Singletons(QC-failed)	0	0
% Singleton	1.7500	0.9200
Diff. Chroms	689024	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	38384828	79868417
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2853173	3252613
Paired Opt. Dupes	18905	36998
% Dupes/100	0.0743	0.0407

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38382868	79802498
Distinct Read Pairs	35529844	76553268
One Read Pair	32857149	73415319
Two Read Pairs	2502495	3032014
NRF = Distinct/Total	0.9257	0.9593
PBC1 = OnePair/Distinct	0.9248	0.9590
PBC2 = OnePair/TwoPair	13.1298	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	71063310	153231608
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71063310	153231608
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	71063310	153231608
Paired(QC-failed)	0	0
Read1	35531655	76615804
Read1(QC-failed)	0	0
Read2	35531655	76615804
Read2(QC-failed)	0	0
Properly Paired	71063310	153231608
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	71063310	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	41233
Np	0
N optimal	41233
N conservative	41233
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.	210
Corr. Est. Fragment Len.	0.3867
Phantom Peak	55
Corr. Phantom Peak	0.3597
Argmin. Corr.	1500
Min. Corr.	0.1987
NSC	1.9464
RSC	1.1676

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	0.6095

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	0.1178
AUC	0.4941
CHANCE divergence	0.1478
Elbow Point	0.0000
JS Distance	0.9322
Synthetic AUC	0.5042
Synthetic Elbow Point	0.5631
Synthetic JS Distance	0.6105