Untitled

No description

Report generated at 2020-06-05 10:40:38

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	43490134	94272842
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	42735055	92659557
Mapped(QC-failed)	0	0
% Mapped	98.2600	98.2900
Paired	43490134	94272842
Paired(QC-failed)	0	0
Read1	21745067	47136421
Read1(QC-failed)	0	0
Read2	21745067	47136421
Read2(QC-failed)	0	0
Properly Paired	42495675	91574742
Properly Paired(QC-failed)	0	0
% Properly Paired	97.7100	97.1400
With itself	42592850	92304558
With itself(QC-failed)	0	0
Singletons	142205	354999
Singletons(QC-failed)	0	0
% Singleton	0.3300	0.3800
Diff. Chroms	32107	370286
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	19594072	40575988
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4810457	1257392
Paired Opt. Dupes	1258	3763
% Dupes/100	0.2455	0.0310

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	19582022	40180957
Distinct Read Pairs	14774697	38989114
One Read Pair	11539390	37836528
Two Read Pairs	2240556	1116568
NRF = Distinct/Total	0.7545	0.9703
PBC1 = OnePair/Distinct	0.7810	0.9704
PBC2 = OnePair/TwoPair	5.1502	33.8865

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	29567230	78637192
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	29567230	78637192
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	29567230	78637192
Paired(QC-failed)	0	0
Read1	14783615	39318596
Read1(QC-failed)	0	0
Read2	14783615	39318596
Read2(QC-failed)	0	0
Properly Paired	29567230	78637192
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	29567230	78637192
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	124294
Np	0
N optimal	124294
N conservative	124294
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.	0.1525
Phantom Peak	50
Corr. Phantom Peak	0.1538
Argmin. Corr.	1500
Min. Corr.	0.1364
NSC	1.1178
RSC	0.9236

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	0.1453

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	0.2232
AUC	0.4925
CHANCE divergence	0.2078
Elbow Point	0.0000
JS Distance	0.6315
Synthetic AUC	0.5053
Synthetic Elbow Point	0.1800
Synthetic JS Distance	0.3188