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Report generated at 2021-10-24 10:44:15

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	237395296	297361170
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	226917388	291047932
Mapped(QC-failed)	0	0
% Mapped	95.5900	97.8800
Paired	237395296	297361170
Paired(QC-failed)	0	0
Read1	118697648	148680585
Read1(QC-failed)	0	0
Read2	118697648	148680585
Read2(QC-failed)	0	0
Properly Paired	218287918	280334875
Properly Paired(QC-failed)	0	0
% Properly Paired	91.9500	94.2700
With itself	223331861	288800610
With itself(QC-failed)	0	0
Singletons	3585527	2247322
Singletons(QC-failed)	0	0
% Singleton	1.5100	0.7600
Diff. Chroms	2262453	6137618
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	77518597	117478324
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6747358	8499398
Paired Opt. Dupes	29883	27800
% Dupes/100	0.0870	0.0723

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	77517495	117374697
Distinct Read Pairs	70770229	108884086
One Read Pair	64539821	100890040
Two Read Pairs	5754401	7526259
NRF = Distinct/Total	0.9130	0.9277
PBC1 = OnePair/Distinct	0.9120	0.9266
PBC2 = OnePair/TwoPair	11.2157	13.4051

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	141542478	217957852
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	141542478	217957852
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	141542478	217957852
Paired(QC-failed)	0	0
Read1	70771239	108978926
Read1(QC-failed)	0	0
Read2	70771239	108978926
Read2(QC-failed)	0	0
Properly Paired	141542478	217957852
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	141542478	217957852
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	208529
Np	0
N optimal	208529
N conservative	208529
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.	130
Corr. Est. Fragment Len.	0.1904
Phantom Peak	50
Corr. Phantom Peak	0.2251
Argmin. Corr.	1500
Min. Corr.	0.1822
NSC	1.0448
RSC	0.1906

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	0.2880

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	0.2167
AUC	0.4958
CHANCE divergence	0.1216
Elbow Point	0.0000
JS Distance	0.6237
Synthetic AUC	0.5026
Synthetic Elbow Point	0.2831
Synthetic JS Distance	0.3860