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Report generated at 2020-07-10 08:21:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	137219986	172997562
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	135441385	170514341
Mapped(QC-failed)	0	0
% Mapped	98.7000	98.5600
Paired	137219986	172997562
Paired(QC-failed)	0	0
Read1	68609993	86498781
Read1(QC-failed)	0	0
Read2	68609993	86498781
Read2(QC-failed)	0	0
Properly Paired	133349026	165526176
Properly Paired(QC-failed)	0	0
% Properly Paired	97.1800	95.6800
With itself	134892282	169780024
With itself(QC-failed)	0	0
Singletons	549103	734317
Singletons(QC-failed)	0	0
% Singleton	0.4000	0.4200
Diff. Chroms	95778	214733
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	58521714	72844563
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	809146	589909
Paired Opt. Dupes	3163	3866
% Dupes/100	0.0138	0.0081

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	58459120	72728950
Distinct Read Pairs	57660998	72170728
One Read Pair	56885639	71649358
Two Read Pairs	759424	508600
NRF = Distinct/Total	0.9863	0.9923
PBC1 = OnePair/Distinct	0.9866	0.9928
PBC2 = OnePair/TwoPair	74.9063	140.8757

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	115425136	144509308
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	115425136	144509308
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	115425136	144509308
Paired(QC-failed)	0	0
Read1	57712568	72254654
Read1(QC-failed)	0	0
Read2	57712568	72254654
Read2(QC-failed)	0	0
Properly Paired	115425136	144509308
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	115425136	144509308
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	162259
Np	0
N optimal	162259
N conservative	162259
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.	0.1803
Phantom Peak	50
Corr. Phantom Peak	0.1839
Argmin. Corr.	1500
Min. Corr.	0.1746
NSC	1.0328
RSC	0.6142

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	0.1174

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	0.2784
AUC	0.4962
CHANCE divergence	0.1003
Elbow Point	0.0000
JS Distance	0.5861
Synthetic AUC	0.4976
Synthetic Elbow Point	0.1473
Synthetic JS Distance	0.2835