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Report generated at 2020-06-06 04:23:37

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	119936570	139413336
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	117285673	137076202
Mapped(QC-failed)	0	0
% Mapped	97.7900	98.3200
Paired	119936570	139413336
Paired(QC-failed)	0	0
Read1	59968285	69706668
Read1(QC-failed)	0	0
Read2	59968285	69706668
Read2(QC-failed)	0	0
Properly Paired	116453000	135724007
Properly Paired(QC-failed)	0	0
% Properly Paired	97.1000	97.3500
With itself	116944785	136521817
With itself(QC-failed)	0	0
Singletons	340888	554385
Singletons(QC-failed)	0	0
% Singleton	0.2800	0.4000
Diff. Chroms	70170	331576
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	54819521	59910556
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10038053	3644145
Paired Opt. Dupes	3011	3362
% Dupes/100	0.1831	0.0608

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54818918	59868704
Distinct Read Pairs	44780977	56228098
One Read Pair	36336053	52787644
Two Read Pairs	7080605	3261892
NRF = Distinct/Total	0.8169	0.9392
PBC1 = OnePair/Distinct	0.8114	0.9388
PBC2 = OnePair/TwoPair	5.1318	16.1831

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	89562936	112532822
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	89562936	112532822
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	89562936	112532822
Paired(QC-failed)	0	0
Read1	44781468	56266411
Read1(QC-failed)	0	0
Read2	44781468	56266411
Read2(QC-failed)	0	0
Properly Paired	89562936	112532822
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	89562936	112532822
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	98223
Np	0
N optimal	98223
N conservative	98223
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.	145
Corr. Est. Fragment Len.	0.4436
Phantom Peak	55
Corr. Phantom Peak	0.3870
Argmin. Corr.	1500
Min. Corr.	0.2185
NSC	2.0296
RSC	1.3360

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	0.6951

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	0.0660
AUC	0.4957
CHANCE divergence	0.2909
Elbow Point	0.0000
JS Distance	0.8748
Synthetic AUC	0.4960
Synthetic Elbow Point	0.5812
Synthetic JS Distance	0.6668