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Report generated at 2020-05-13 17:58:24

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	88697294	78498540
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	73728122	74844187
Mapped(QC-failed)	0	0
% Mapped	83.1200	95.3400
Paired	88697294	78498540
Paired(QC-failed)	0	0
Read1	44348647	39249270
Read1(QC-failed)	0	0
Read2	44348647	39249270
Read2(QC-failed)	0	0
Properly Paired	69082256	67679938
Properly Paired(QC-failed)	0	0
% Properly Paired	77.8900	86.2200
With itself	70868178	72834832
With itself(QC-failed)	0	0
Singletons	2859944	2009355
Singletons(QC-failed)	0	0
% Singleton	3.2200	2.5600
Diff. Chroms	1206468	3424690
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	29560321	28005715
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1039455	528129
Paired Opt. Dupes	2925	2652
% Dupes/100	0.0352	0.0189

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	29554674	28000939
Distinct Read Pairs	28515423	27472963
One Read Pair	27506968	26953277
Two Read Pairs	978478	511504
NRF = Distinct/Total	0.9648	0.9811
PBC1 = OnePair/Distinct	0.9646	0.9811
PBC2 = OnePair/TwoPair	28.1120	52.6942

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	57041732	54955172
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	57041732	54955172
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	57041732	54955172
Paired(QC-failed)	0	0
Read1	28520866	27477586
Read1(QC-failed)	0	0
Read2	28520866	27477586
Read2(QC-failed)	0	0
Properly Paired	57041732	54955172
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	57041732	54955172
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	75997
Np	0
N optimal	75997
N conservative	75997
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.	250
Corr. Est. Fragment Len.	0.2103
Phantom Peak	50
Corr. Phantom Peak	0.2055
Argmin. Corr.	1500
Min. Corr.	0.1913
NSC	1.0993
RSC	1.3403

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	0.1863

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	0.1359
AUC	0.4946
CHANCE divergence	0.4080
Elbow Point	0.0000
JS Distance	0.6873
Synthetic AUC	0.5052
Synthetic Elbow Point	0.1095
Synthetic JS Distance	0.4113