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Report generated at 2020-05-13 23:53:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	56660188	153902130
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54003485	147991110
Mapped(QC-failed)	0	0
% Mapped	95.3100	96.1600
Paired	56660188	153902130
Paired(QC-failed)	0	0
Read1	28330094	76951065
Read1(QC-failed)	0	0
Read2	28330094	76951065
Read2(QC-failed)	0	0
Properly Paired	51304142	138621783
Properly Paired(QC-failed)	0	0
% Properly Paired	90.5500	90.0700
With itself	52929998	144978594
With itself(QC-failed)	0	0
Singletons	1073487	3012516
Singletons(QC-failed)	0	0
% Singleton	1.8900	1.9600
Diff. Chroms	1179216	4251163
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	22676270	58423843
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	183121	818600
Paired Opt. Dupes	2082	6310
% Dupes/100	0.0081	0.0140

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22676180	58422690
Distinct Read Pairs	22493059	57604109
One Read Pair	22311168	56795332
Two Read Pairs	180675	799080
NRF = Distinct/Total	0.9919	0.9860
PBC1 = OnePair/Distinct	0.9919	0.9860
PBC2 = OnePair/TwoPair	123.4879	71.0759

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	44986298	115210486
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	44986298	115210486
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	44986298	115210486
Paired(QC-failed)	0	0
Read1	22493149	57605243
Read1(QC-failed)	0	0
Read2	22493149	57605243
Read2(QC-failed)	0	0
Properly Paired	44986298	115210486
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	44986298	115210486
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	102259
Np	0
N optimal	102259
N conservative	102259
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.	250
Corr. Est. Fragment Len.	0.2175
Phantom Peak	50
Corr. Phantom Peak	0.2073
Argmin. Corr.	1500
Min. Corr.	0.1908
NSC	1.1400
RSC	1.6137

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	0.3423

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	0.1237
AUC	0.4939
CHANCE divergence	0.3962
Elbow Point	0.0000
JS Distance	0.7142
Synthetic AUC	0.4953
Synthetic Elbow Point	0.2113
Synthetic JS Distance	0.4478