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Report generated at 2021-03-18 11:21:04

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	63390866	107748822
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	57473746	105210529
Mapped(QC-failed)	0	0
% Mapped	90.6700	97.6400
Paired	63390866	107748822
Paired(QC-failed)	0	0
Read1	31695433	53874411
Read1(QC-failed)	0	0
Read2	31695433	53874411
Read2(QC-failed)	0	0
Properly Paired	56110913	89353817
Properly Paired(QC-failed)	0	0
% Properly Paired	88.5200	82.9300
With itself	57144866	104162194
With itself(QC-failed)	0	0
Singletons	328880	1048335
Singletons(QC-failed)	0	0
% Singleton	0.5200	0.9700
Diff. Chroms	367029	11301530
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	25896094	39900791
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3095602	469856
Paired Opt. Dupes	2103	1823
% Dupes/100	0.1195	0.0118

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	25893760	39896493
Distinct Read Pairs	22798413	39426880
One Read Pair	20303650	38982156
Two Read Pairs	2174281	431298
NRF = Distinct/Total	0.8805	0.9882
PBC1 = OnePair/Distinct	0.8906	0.9887
PBC2 = OnePair/TwoPair	9.3381	90.3833

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	45600984	78861870
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45600984	78861870
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	45600984	78861870
Paired(QC-failed)	0	0
Read1	22800492	39430935
Read1(QC-failed)	0	0
Read2	22800492	39430935
Read2(QC-failed)	0	0
Properly Paired	45600984	78861870
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	45600984	78861870
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	62066
Np	0
N optimal	62066
N conservative	62066
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.	160
Corr. Est. Fragment Len.	0.2656
Phantom Peak	55
Corr. Phantom Peak	0.2075
Argmin. Corr.	1500
Min. Corr.	0.1382
NSC	1.9222
RSC	1.8384

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	0.4267

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	0.1603
AUC	0.4940
CHANCE divergence	0.1742
Elbow Point	0.0000
JS Distance	0.7946
Synthetic AUC	0.5071
Synthetic Elbow Point	0.4019
Synthetic JS Distance	0.4945