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Report generated at 2020-06-06 19:13:31

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	148838176	139413336
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	135774191	137076202
Mapped(QC-failed)	0	0
% Mapped	91.2200	98.3200
Paired	148838176	139413336
Paired(QC-failed)	0	0
Read1	74419088	69706668
Read1(QC-failed)	0	0
Read2	74419088	69706668
Read2(QC-failed)	0	0
Properly Paired	131664587	135724007
Properly Paired(QC-failed)	0	0
% Properly Paired	88.4600	97.3500
With itself	133479824	136521817
With itself(QC-failed)	0	0
Singletons	2294367	554385
Singletons(QC-failed)	0	0
% Singleton	1.5400	0.4000
Diff. Chroms	256224	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	43754158	59910556
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	17621854	3644145
Paired Opt. Dupes	2639	3362
% Dupes/100	0.4027	0.0608

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43753211	59868704
Distinct Read Pairs	26131734	56228098
One Read Pair	14883397	52787644
Two Read Pairs	7000702	3261892
NRF = Distinct/Total	0.5973	0.9392
PBC1 = OnePair/Distinct	0.5696	0.9388
PBC2 = OnePair/TwoPair	2.1260	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	52264608	112532822
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52264608	112532822
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	52264608	112532822
Paired(QC-failed)	0	0
Read1	26132304	56266411
Read1(QC-failed)	0	0
Read2	26132304	56266411
Read2(QC-failed)	0	0
Properly Paired	52264608	112532822
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	52264608	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	193931
Np	0
N optimal	193931
N conservative	193931
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.	135
Corr. Est. Fragment Len.	0.2081
Phantom Peak	50
Corr. Phantom Peak	0.2658
Argmin. Corr.	1500
Min. Corr.	0.1926
NSC	1.0802
RSC	0.2112

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	0.3196

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	0.1655
AUC	0.4944
CHANCE divergence	0.2614
Elbow Point	0.0000
JS Distance	0.6870
Synthetic AUC	0.5105
Synthetic Elbow Point	0.2609
Synthetic JS Distance	0.4152