Untitled

No description

Report generated at 2020-05-21 01:30:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	139105618	172040776
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100085510	166313177
Mapped(QC-failed)	0	0
% Mapped	71.9500	96.6700
Paired	139105618	172040776
Paired(QC-failed)	0	0
Read1	69552809	86020388
Read1(QC-failed)	0	0
Read2	69552809	86020388
Read2(QC-failed)	0	0
Properly Paired	98519049	164316966
Properly Paired(QC-failed)	0	0
% Properly Paired	70.8200	95.5100
With itself	99047421	165368990
With itself(QC-failed)	0	0
Singletons	1038089	944187
Singletons(QC-failed)	0	0
% Singleton	0.7500	0.5500
Diff. Chroms	185322	377471
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	42855638	70615481
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	465249	448995
Paired Opt. Dupes	2459	1973
% Dupes/100	0.0109	0.0064

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42850612	70604488
Distinct Read Pairs	42385426	70155597
One Read Pair	41925633	69710274
Two Read Pairs	454503	441873
NRF = Distinct/Total	0.9891	0.9936
PBC1 = OnePair/Distinct	0.9892	0.9937
PBC2 = OnePair/TwoPair	92.2450	157.7609

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	84780778	140332972
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84780778	140332972
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84780778	140332972
Paired(QC-failed)	0	0
Read1	42390389	70166486
Read1(QC-failed)	0	0
Read2	42390389	70166486
Read2(QC-failed)	0	0
Properly Paired	84780778	140332972
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84780778	140332972
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	170315
Np	0
N optimal	170315
N conservative	170315
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.	0.1830
Phantom Peak	50
Corr. Phantom Peak	0.2125
Argmin. Corr.	1500
Min. Corr.	0.1725
NSC	1.0608
RSC	0.2622

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	0.1360

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	0.2428
AUC	0.4956
CHANCE divergence	0.1193
Elbow Point	0.0000
JS Distance	0.6263
Synthetic AUC	0.5000
Synthetic Elbow Point	0.1431
Synthetic JS Distance	0.3343