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Report generated at 2021-10-21 17:36:06

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	199933616	249846494
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	195953604	245693039
Mapped(QC-failed)	0	0
% Mapped	98.0100	98.3400
Paired	199933616	249846494
Paired(QC-failed)	0	0
Read1	99966808	124923247
Read1(QC-failed)	0	0
Read2	99966808	124923247
Read2(QC-failed)	0	0
Properly Paired	191096590	234957962
Properly Paired(QC-failed)	0	0
% Properly Paired	95.5800	94.0400
With itself	194204318	243593650
With itself(QC-failed)	0	0
Singletons	1749286	2099389
Singletons(QC-failed)	0	0
% Singleton	0.8700	0.8400
Diff. Chroms	1940951	6531607
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	76779095	98092949
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7598586	7176563
Paired Opt. Dupes	71713	57044
% Dupes/100	0.0990	0.0732

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	76777351	98012771
Distinct Read Pairs	69178941	90842894
One Read Pair	62211841	84087873
Two Read Pairs	6383202	6363556
NRF = Distinct/Total	0.9010	0.9268
PBC1 = OnePair/Distinct	0.8993	0.9256
PBC2 = OnePair/TwoPair	9.7462	13.2140

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	138361018	181832772
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	138361018	181832772
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	138361018	181832772
Paired(QC-failed)	0	0
Read1	69180509	90916386
Read1(QC-failed)	0	0
Read2	69180509	90916386
Read2(QC-failed)	0	0
Properly Paired	138361018	181832772
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	138361018	181832772
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	257751
Np	0
N optimal	257751
N conservative	257751
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.	210
Corr. Est. Fragment Len.	0.1794
Phantom Peak	50
Corr. Phantom Peak	0.1874
Argmin. Corr.	1500
Min. Corr.	0.1752
NSC	1.0240
RSC	0.3440

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	0.2983

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	0.2270
AUC	0.4958
CHANCE divergence	0.1164
Elbow Point	0.0000
JS Distance	0.6031
Synthetic AUC	0.5010
Synthetic Elbow Point	0.2568
Synthetic JS Distance	0.3717