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Report generated at 2020-05-10 12:16:54

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	54889502	94394890
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50942111	90679650
Mapped(QC-failed)	0	0
% Mapped	92.8100	96.0600
Paired	54889502	94394890
Paired(QC-failed)	0	0
Read1	27444751	47197445
Read1(QC-failed)	0	0
Read2	27444751	47197445
Read2(QC-failed)	0	0
Properly Paired	49497425	85747226
Properly Paired(QC-failed)	0	0
% Properly Paired	90.1800	90.8400
With itself	49999877	88391054
With itself(QC-failed)	0	0
Singletons	942234	2288596
Singletons(QC-failed)	0	0
% Singleton	1.7200	2.4200
Diff. Chroms	279258	1671322
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	21587436	36214131
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	266457	344208
Paired Opt. Dupes	3311	1746
% Dupes/100	0.0123	0.0095

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	21586593	36209957
Distinct Read Pairs	21320143	35865787
One Read Pair	21056479	35524443
Two Read Pairs	260906	338545
NRF = Distinct/Total	0.9877	0.9905
PBC1 = OnePair/Distinct	0.9876	0.9905
PBC2 = OnePair/TwoPair	80.7052	104.9327

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	42641958	71739846
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	42641958	71739846
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	42641958	71739846
Paired(QC-failed)	0	0
Read1	21320979	35869923
Read1(QC-failed)	0	0
Read2	21320979	35869923
Read2(QC-failed)	0	0
Properly Paired	42641958	71739846
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	42641958	71739846
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	32830
Np	0
N optimal	32830
N conservative	32830
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.	255
Corr. Est. Fragment Len.	0.2546
Phantom Peak	50
Corr. Phantom Peak	0.2477
Argmin. Corr.	1500
Min. Corr.	0.1802
NSC	1.4128
RSC	1.1025

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	0.3172

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	0.1663
AUC	0.4937
CHANCE divergence	0.2483
Elbow Point	0.0000
JS Distance	0.6902
Synthetic AUC	0.4970
Synthetic Elbow Point	0.3070
Synthetic JS Distance	0.4440