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Report generated at 2020-05-18 11:23:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	159396982	91058302
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	154790524	88858777
Mapped(QC-failed)	0	0
% Mapped	97.1100	97.5800
Paired	159396982	91058302
Paired(QC-failed)	0	0
Read1	79698491	45529151
Read1(QC-failed)	0	0
Read2	79698491	45529151
Read2(QC-failed)	0	0
Properly Paired	153144243	87463672
Properly Paired(QC-failed)	0	0
% Properly Paired	96.0800	96.0500
With itself	154220486	88414762
With itself(QC-failed)	0	0
Singletons	570038	444015
Singletons(QC-failed)	0	0
% Singleton	0.3600	0.4900
Diff. Chroms	644491	473257
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	70743477	38226012
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	523813	140477
Paired Opt. Dupes	2951	1407
% Dupes/100	0.0074	0.0037

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	70733044	38152882
Distinct Read Pairs	70209332	38013834
One Read Pair	69689713	37875216
Two Read Pairs	515559	138191
NRF = Distinct/Total	0.9926	0.9964
PBC1 = OnePair/Distinct	0.9926	0.9964
PBC2 = OnePair/TwoPair	135.1731	274.0787

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	140439328	76171070
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	140439328	76171070
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	140439328	76171070
Paired(QC-failed)	0	0
Read1	70219664	38085535
Read1(QC-failed)	0	0
Read2	70219664	38085535
Read2(QC-failed)	0	0
Properly Paired	140439328	76171070
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	140439328	76171070
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	246134
Np	0
N optimal	246134
N conservative	246134
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.	160
Corr. Est. Fragment Len.	0.1997
Phantom Peak	50
Corr. Phantom Peak	0.2008
Argmin. Corr.	1500
Min. Corr.	0.1853
NSC	1.0777
RSC	0.9291

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	0.4323

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	0.1728
AUC	0.4966
CHANCE divergence	0.1262
Elbow Point	0.0000
JS Distance	0.7408
Synthetic AUC	0.4977
Synthetic Elbow Point	0.2710
Synthetic JS Distance	0.4616