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Report generated at 2019-10-13 04:16:34

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	91153108	87738496
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	89450653	86229239
Mapped(QC-failed)	0	0
% Mapped	98.1300	98.2800
Paired	91153108	87738496
Paired(QC-failed)	0	0
Read1	45576554	43869248
Read1(QC-failed)	0	0
Read2	45576554	43869248
Read2(QC-failed)	0	0
Properly Paired	88191258	85110249
Properly Paired(QC-failed)	0	0
% Properly Paired	96.7500	97.0000
With itself	88790663	85780325
With itself(QC-failed)	0	0
Singletons	659990	448914
Singletons(QC-failed)	0	0
% Singleton	0.7200	0.5100
Diff. Chroms	193608	132532
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	38892423	37459366
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2521641	810815
Paired Opt. Dupes	12804	14619
% Dupes/100	0.0648	0.0216

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38891643	37393436
Distinct Read Pairs	36370057	36585669
One Read Pair	33995801	35798621
Two Read Pairs	2235324	769016
NRF = Distinct/Total	0.9352	0.9784
PBC1 = OnePair/Distinct	0.9347	0.9785
PBC2 = OnePair/TwoPair	15.2084	46.5512

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	72741564	73297102
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	72741564	73297102
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	72741564	73297102
Paired(QC-failed)	0	0
Read1	36370782	36648551
Read1(QC-failed)	0	0
Read2	36370782	36648551
Read2(QC-failed)	0	0
Properly Paired	72741564	73297102
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	72741564	73297102
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	78656
Np	0
N optimal	78656
N conservative	78656
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.	135
Corr. Est. Fragment Len.	0.1705
Phantom Peak	50
Corr. Phantom Peak	0.1773
Argmin. Corr.	1500
Min. Corr.	0.1671
NSC	1.0202
RSC	0.3330

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	0.0653

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	0.3072
AUC	0.4952
CHANCE divergence	0.1004
Elbow Point	0.0000
JS Distance	0.5602
Synthetic AUC	0.4972
Synthetic Elbow Point	0.0630
Synthetic JS Distance	0.2343