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Report generated at 2019-10-13 17:52:05

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	130554886	90571450
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	101409709	89141373
Mapped(QC-failed)	0	0
% Mapped	77.6800	98.4200
Paired	130554886	90571450
Paired(QC-failed)	0	0
Read1	65277443	45285725
Read1(QC-failed)	0	0
Read2	65277443	45285725
Read2(QC-failed)	0	0
Properly Paired	97825431	88372908
Properly Paired(QC-failed)	0	0
% Properly Paired	74.9300	97.5700
With itself	99387866	88783529
With itself(QC-failed)	0	0
Singletons	2021843	357844
Singletons(QC-failed)	0	0
% Singleton	1.5500	0.4000
Diff. Chroms	163602	165137
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	34355324	39015967
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2347181	627860
Paired Opt. Dupes	3153	3635
% Dupes/100	0.0683	0.0161

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34348844	38965090
Distinct Read Pairs	32002074	38338878
One Read Pair	29816093	37724707
Two Read Pairs	2041684	603360
NRF = Distinct/Total	0.9317	0.9839
PBC1 = OnePair/Distinct	0.9317	0.9840
PBC2 = OnePair/TwoPair	14.6037	62.5244

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	64016286	76776214
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	64016286	76776214
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	64016286	76776214
Paired(QC-failed)	0	0
Read1	32008143	38388107
Read1(QC-failed)	0	0
Read2	32008143	38388107
Read2(QC-failed)	0	0
Properly Paired	64016286	76776214
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	64016286	76776214
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	164142
Np	0
N optimal	164142
N conservative	164142
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.	120
Corr. Est. Fragment Len.	0.1968
Phantom Peak	50
Corr. Phantom Peak	0.2548
Argmin. Corr.	1500
Min. Corr.	0.1844
NSC	1.0669
RSC	0.1753

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	0.2199

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	0.2386
AUC	0.4949
CHANCE divergence	0.1135
Elbow Point	0.0000
JS Distance	0.6699
Synthetic AUC	0.4967
Synthetic Elbow Point	0.1994
Synthetic JS Distance	0.3469