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Report generated at 2022-01-13 05:33:21

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	36431612	52208364
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	28865628	46961269
Mapped(QC-failed)	0	0
% Mapped	79.2300	89.9500
Paired	36431612	52208364
Paired(QC-failed)	0	0
Read1	18215806	26104182
Read1(QC-failed)	0	0
Read2	18215806	26104182
Read2(QC-failed)	0	0
Properly Paired	27287953	38339710
Properly Paired(QC-failed)	0	0
% Properly Paired	74.9000	73.4400
With itself	27902416	44775897
With itself(QC-failed)	0	0
Singletons	963212	2185372
Singletons(QC-failed)	0	0
% Singleton	2.6400	4.1900
Diff. Chroms	470494	4612399
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	12068765	13624196
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	493953	312822
Paired Opt. Dupes	2709	3040
% Dupes/100	0.0409	0.0230

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	12067039	13619156
Distinct Read Pairs	11573175	13306524
One Read Pair	11097092	13000280
Two Read Pairs	458887	300008
NRF = Distinct/Total	0.9591	0.9770
PBC1 = OnePair/Distinct	0.9589	0.9770
PBC2 = OnePair/TwoPair	24.1826	43.3331

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	23149624	26622748
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	23149624	26622748
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	23149624	26622748
Paired(QC-failed)	0	0
Read1	11574812	13311374
Read1(QC-failed)	0	0
Read2	11574812	13311374
Read2(QC-failed)	0	0
Properly Paired	23149624	26622748
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	23149624	26622748
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	26482
Np	0
N optimal	26482
N conservative	26482
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 (14M)

	rep1
Reads	14844009
Est. Fragment Len.	280
Corr. Est. Fragment Len.	0.4347
Phantom Peak	55
Corr. Phantom Peak	0.3728
Argmin. Corr.	1500
Min. Corr.	0.2033
NSC	2.1382
RSC	1.3653

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	0.6526

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	0.0553
AUC	0.4914
CHANCE divergence	0.5104
Elbow Point	0.0000
JS Distance	0.8804
Synthetic AUC	0.5061
Synthetic Elbow Point	0.5019
Synthetic JS Distance	0.6426