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Report generated at 2020-05-13 07:58:39

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	60077482	51927324
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50467693	49878862
Mapped(QC-failed)	0	0
% Mapped	84.0000	96.0600
Paired	60077482	51927324
Paired(QC-failed)	0	0
Read1	30038741	25963662
Read1(QC-failed)	0	0
Read2	30038741	25963662
Read2(QC-failed)	0	0
Properly Paired	48365726	47781548
Properly Paired(QC-failed)	0	0
% Properly Paired	80.5100	92.0200
With itself	49212582	49123727
With itself(QC-failed)	0	0
Singletons	1255111	755135
Singletons(QC-failed)	0	0
% Singleton	2.0900	1.4500
Diff. Chroms	408948	883965
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	21173766	20969721
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	325788	326676
Paired Opt. Dupes	3045	2745
% Dupes/100	0.0154	0.0156

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	21172641	20965217
Distinct Read Pairs	20846866	20638613
One Read Pair	20525421	20316429
Two Read Pairs	317169	317829
NRF = Distinct/Total	0.9846	0.9844
PBC1 = OnePair/Distinct	0.9846	0.9844
PBC2 = OnePair/TwoPair	64.7145	63.9225

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	41695956	41286090
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	41695956	41286090
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	41695956	41286090
Paired(QC-failed)	0	0
Read1	20847978	20643045
Read1(QC-failed)	0	0
Read2	20847978	20643045
Read2(QC-failed)	0	0
Properly Paired	41695956	41286090
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	41695956	41286090
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	88962
Np	0
N optimal	88962
N conservative	88962
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.	285
Corr. Est. Fragment Len.	0.1842
Phantom Peak	50
Corr. Phantom Peak	0.1867
Argmin. Corr.	1500
Min. Corr.	0.1719
NSC	1.0718
RSC	0.8303

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	0.1182

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	0.1825
AUC	0.4937
CHANCE divergence	0.3187
Elbow Point	0.0000
JS Distance	0.6321
Synthetic AUC	0.5003
Synthetic Elbow Point	0.0657
Synthetic JS Distance	0.3449