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Report generated at 2020-05-31 10:38:10

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	179767606	246240780
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	178422010	242844910
Mapped(QC-failed)	0	0
% Mapped	99.2500	98.6200
Paired	179767606	246240780
Paired(QC-failed)	0	0
Read1	89883803	123120390
Read1(QC-failed)	0	0
Read2	89883803	123120390
Read2(QC-failed)	0	0
Properly Paired	177475877	234365232
Properly Paired(QC-failed)	0	0
% Properly Paired	98.7300	95.1800
With itself	177776739	241490309
With itself(QC-failed)	0	0
Singletons	645271	1354601
Singletons(QC-failed)	0	0
% Singleton	0.3600	0.5500
Diff. Chroms	51087	217954
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	82145469	104467932
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2108731	1214384
Paired Opt. Dupes	5314	3855
% Dupes/100	0.0257	0.0116

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	82135428	104430742
Distinct Read Pairs	80027153	103222930
One Read Pair	78016814	102080800
Two Read Pairs	1930139	1115539
NRF = Distinct/Total	0.9743	0.9884
PBC1 = OnePair/Distinct	0.9749	0.9889
PBC2 = OnePair/TwoPair	40.4203	91.5081

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	160073476	206507096
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	160073476	206507096
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	160073476	206507096
Paired(QC-failed)	0	0
Read1	80036738	103253548
Read1(QC-failed)	0	0
Read2	80036738	103253548
Read2(QC-failed)	0	0
Properly Paired	160073476	206507096
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	160073476	206507096
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	155999
Np	0
N optimal	155999
N conservative	155999
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.	150
Corr. Est. Fragment Len.	0.1940
Phantom Peak	45
Corr. Phantom Peak	0.1845
Argmin. Corr.	1500
Min. Corr.	0.1770
NSC	1.0962
RSC	2.2678

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	0.5322

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	0.1780
AUC	0.4968
CHANCE divergence	0.1041
Elbow Point	0.0000
JS Distance	0.8021
Synthetic AUC	0.5044
Synthetic Elbow Point	0.3677
Synthetic JS Distance	0.4656