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Report generated at 2021-02-06 09:04:37

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	126732858	106653906
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	122188990	104801407
Mapped(QC-failed)	0	0
% Mapped	96.4100	98.2600
Paired	126732858	106653906
Paired(QC-failed)	0	0
Read1	63366429	53326953
Read1(QC-failed)	0	0
Read2	63366429	53326953
Read2(QC-failed)	0	0
Properly Paired	118076802	102958254
Properly Paired(QC-failed)	0	0
% Properly Paired	93.1700	96.5300
With itself	120825344	104098130
With itself(QC-failed)	0	0
Singletons	1363646	703277
Singletons(QC-failed)	0	0
% Singleton	1.0800	0.6600
Diff. Chroms	247954	170230
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	42346001	44220133
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	693664	314126
Paired Opt. Dupes	58730	110501
% Dupes/100	0.0164	0.0071

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42330752	44206086
Distinct Read Pairs	41637741	43892511
One Read Pair	41098203	43597064
Two Read Pairs	506206	288605
NRF = Distinct/Total	0.9836	0.9929
PBC1 = OnePair/Distinct	0.9870	0.9933
PBC2 = OnePair/TwoPair	81.1887	151.0614

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	83304674	87812014
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	83304674	87812014
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	83304674	87812014
Paired(QC-failed)	0	0
Read1	41652337	43906007
Read1(QC-failed)	0	0
Read2	41652337	43906007
Read2(QC-failed)	0	0
Properly Paired	83304674	87812014
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	83304674	87812014
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	254720
Np	0
N optimal	254720
N conservative	254720
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.	125
Corr. Est. Fragment Len.	0.1948
Phantom Peak	50
Corr. Phantom Peak	0.2168
Argmin. Corr.	1500
Min. Corr.	0.1799
NSC	1.0826
RSC	0.4034

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	0.3657

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	0.1920
AUC	0.4954
CHANCE divergence	0.1358
Elbow Point	0.0000
JS Distance	0.7110
Synthetic AUC	0.4996
Synthetic Elbow Point	0.2128
Synthetic JS Distance	0.4172