Untitled

No description

Report generated at 2020-06-06 01:57:10

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	149930166	94259596
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	146164473	92701160
Mapped(QC-failed)	0	0
% Mapped	97.4900	98.3500
Paired	149930166	94259596
Paired(QC-failed)	0	0
Read1	74965083	47129798
Read1(QC-failed)	0	0
Read2	74965083	47129798
Read2(QC-failed)	0	0
Properly Paired	144307650	91902141
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2500	97.5000
With itself	145099650	92320316
With itself(QC-failed)	0	0
Singletons	1064823	380844
Singletons(QC-failed)	0	0
% Singleton	0.7100	0.4000
Diff. Chroms	179004	138740
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	60694588	40550057
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7615308	1766985
Paired Opt. Dupes	4321	3621
% Dupes/100	0.1255	0.0436

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	60693842	40529364
Distinct Read Pairs	53078625	38763430
One Read Pair	46391915	37080130
Two Read Pairs	5875178	1606781
NRF = Distinct/Total	0.8745	0.9564
PBC1 = OnePair/Distinct	0.8740	0.9566
PBC2 = OnePair/TwoPair	7.8963	23.0773

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	106158560	77566144
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	106158560	77566144
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	106158560	77566144
Paired(QC-failed)	0	0
Read1	53079280	38783072
Read1(QC-failed)	0	0
Read2	53079280	38783072
Read2(QC-failed)	0	0
Properly Paired	106158560	77566144
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	106158560	77566144
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	47411
Np	0
N optimal	47411
N conservative	47411
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.	0.1795
Phantom Peak	50
Corr. Phantom Peak	0.2023
Argmin. Corr.	1500
Min. Corr.	0.1738
NSC	1.0329
RSC	0.2011

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	0.0190

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	0.3185
AUC	0.4960
CHANCE divergence	0.1010
Elbow Point	0.0000
JS Distance	0.5234
Synthetic AUC	0.5058
Synthetic Elbow Point	0.0388
Synthetic JS Distance	0.2185