Untitled

No description

Report generated at 2021-06-17 04:56:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	74149064	53199662
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71307929	52346922
Mapped(QC-failed)	0	0
% Mapped	96.1700	98.4000
Paired	74149064	53199662
Paired(QC-failed)	0	0
Read1	37074532	26599831
Read1(QC-failed)	0	0
Read2	37074532	26599831
Read2(QC-failed)	0	0
Properly Paired	70736581	51190080
Properly Paired(QC-failed)	0	0
% Properly Paired	95.4000	96.2200
With itself	71020900	52040805
With itself(QC-failed)	0	0
Singletons	287029	306117
Singletons(QC-failed)	0	0
% Singleton	0.3900	0.5800
Diff. Chroms	30312	93286
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	32408314	22056683
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2600751	107424
Paired Opt. Dupes	49968	40026
% Dupes/100	0.0803	0.0049

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	32407319	22056254
Distinct Read Pairs	29806652	21948832
One Read Pair	27476214	21843816
Two Read Pairs	2126123	103699
NRF = Distinct/Total	0.9198	0.9951
PBC1 = OnePair/Distinct	0.9218	0.9952
PBC2 = OnePair/TwoPair	12.9232	210.6464

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	59615126	43898518
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	59615126	43898518
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	59615126	43898518
Paired(QC-failed)	0	0
Read1	29807563	21949259
Read1(QC-failed)	0	0
Read2	29807563	21949259
Read2(QC-failed)	0	0
Properly Paired	59615126	43898518
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	59615126	43898518
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	117139
Np	0
N optimal	117139
N conservative	117139
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.	145
Corr. Est. Fragment Len.	0.2566
Phantom Peak	55
Corr. Phantom Peak	0.1901
Argmin. Corr.	1500
Min. Corr.	0.1552
NSC	1.6540
RSC	2.9010

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	0.4774

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	0.1461
AUC	0.4946
CHANCE divergence	0.1645
Elbow Point	0.0000
JS Distance	0.8246
Synthetic AUC	0.5085
Synthetic Elbow Point	0.3768
Synthetic JS Distance	0.5153