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Report generated at 2020-05-10 19:04:05

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	59545938	49040330
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	39631506	43899885
Mapped(QC-failed)	0	0
% Mapped	66.5600	89.5200
Paired	59545938	49040330
Paired(QC-failed)	0	0
Read1	29772969	24520165
Read1(QC-failed)	0	0
Read2	29772969	24520165
Read2(QC-failed)	0	0
Properly Paired	22504125	30373686
Properly Paired(QC-failed)	0	0
% Properly Paired	37.7900	61.9400
With itself	36274739	41523513
With itself(QC-failed)	0	0
Singletons	3356767	2376372
Singletons(QC-failed)	0	0
% Singleton	5.6400	4.8500
Diff. Chroms	11181979	7654539
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	5648295	10159811
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	250145	264224
Paired Opt. Dupes	939	1355
% Dupes/100	0.0443	0.0260

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	5647512	10158782
Distinct Read Pairs	5397403	9894586
One Read Pair	5156986	9636269
Two Read Pairs	231075	252589
NRF = Distinct/Total	0.9557	0.9740
PBC1 = OnePair/Distinct	0.9555	0.9739
PBC2 = OnePair/TwoPair	22.3174	38.1500

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	10796300	19791174
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	10796300	19791174
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	10796300	19791174
Paired(QC-failed)	0	0
Read1	5398150	9895587
Read1(QC-failed)	0	0
Read2	5398150	9895587
Read2(QC-failed)	0	0
Properly Paired	10796300	19791174
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	10796300	19791174
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	26469
Np	0
N optimal	26469
N conservative	26469
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.	225
Corr. Est. Fragment Len.	0.1935
Phantom Peak	50
Corr. Phantom Peak	0.2036
Argmin. Corr.	1500
Min. Corr.	0.1637
NSC	1.1824
RSC	0.7472

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	0.0655

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	0.1370
AUC	0.4875
CHANCE divergence	0.4769
Elbow Point	0.0000
JS Distance	0.6629
Synthetic AUC	0.5010
Synthetic Elbow Point	0.1113
Synthetic JS Distance	0.3349