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Report generated at 2021-10-10 18:34:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	97706018	249846494
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	94911844	245693039
Mapped(QC-failed)	0	0
% Mapped	97.1400	98.3400
Paired	97706018	249846494
Paired(QC-failed)	0	0
Read1	48853009	124923247
Read1(QC-failed)	0	0
Read2	48853009	124923247
Read2(QC-failed)	0	0
Properly Paired	93599199	234957962
Properly Paired(QC-failed)	0	0
% Properly Paired	95.8000	94.0400
With itself	94341330	243593650
With itself(QC-failed)	0	0
Singletons	570514	2099389
Singletons(QC-failed)	0	0
% Singleton	0.5800	0.8400
Diff. Chroms	506069	6531607
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	41176126	98092949
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7249195	7176563
Paired Opt. Dupes	25754	57044
% Dupes/100	0.1761	0.0732

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	41172409	0
Distinct Read Pairs	33923839	0
One Read Pair	27757690	0
Two Read Pairs	5227272	0
NRF = Distinct/Total	0.8239	0.0000
PBC1 = OnePair/Distinct	0.8182	0.0000
PBC2 = OnePair/TwoPair	5.3102	-1.0000

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	67853862	181832772
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67853862	181832772
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	67853862	181832772
Paired(QC-failed)	0	0
Read1	33926931	90916386
Read1(QC-failed)	0	0
Read2	33926931	90916386
Read2(QC-failed)	0	0
Properly Paired	67853862	181832772
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	67853862	181832772
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	104471
Np	0
N optimal	104471
N conservative	104471
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.	215
Corr. Est. Fragment Len.	0.2398
Phantom Peak	50
Corr. Phantom Peak	0.2304
Argmin. Corr.	1500
Min. Corr.	0.1911
NSC	1.2552
RSC	1.2416

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	0.5616

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	0.1257
AUC	0.4940
CHANCE divergence	0.1807
Elbow Point	0.0000
JS Distance	0.8258
Synthetic AUC	0.4993
Synthetic Elbow Point	0.4707
Synthetic JS Distance	0.5419