QC Report

	general
Report generated at	2020-05-19 22:15:29
Title	cbf1_eth_exo
Description	chip exo data for cbf1 (ethanol-limited)
Pipeline version	v1.3.6
Pipeline type	tf
Genome	sacCer3
Aligner	bowtie2
Sequencing endedness	{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'ctl1': {'paired_end': True}, 'ctl2': {'paired_end': True}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2
Total Reads	11610724	10454749	3555302	2475684
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	11008302	9954563	1729789	2119384
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	94.8	95.19999999999999	48.699999999999996	85.6
Paired Reads	0	0	3555302	2475684
Paired Reads (QC-failed)	0	0	0	0
Read1	0	0	1777651	1237842
Read1 (QC-failed)	0	0	0	0
Read2	0	0	1777651	1237842
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	0	0	1624258	1980632
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	0.0	0.0	45.7	80.0
With itself	0	0	1628458	1982620
With itself (QC-failed)	0	0	0	0
Singletons	0	0	101331	136764
Singletons (QC-failed)	0	0	0	0
% Singleton	0.0	0.0	2.9000000000000004	5.5
Diff. Chroms	0	0	546	783
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2
Unpaired Reads	9702883	8852105	0	0
Paired Reads	0	0	581306	779111
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	9193459	8462154	0	0
Paired Duplicate Reads	0	0	551622	738554
Paired Optical Duplicate Reads	0	0	0	0
% Duplicate Reads	94.7498	95.5948	94.8936	94.7945

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8, for paired-end)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

SAMstat (filtered/deduped BAM)

	rep1	rep2	ctl1	ctl2
Total Reads	9702883	8852105	1162612	1558222
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	9702883	8852105	1162612	1558222
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0
Paired Reads	0	0	1162612	1558222
Paired Reads (QC-failed)	0	0	0	0
Read1	0	0	581306	779111
Read1 (QC-failed)	0	0	0	0
Read2	0	0	581306	779111
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	0	0	1162612	1558222
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	0.0	0.0	100.0	100.0
With itself	0	0	1162612	1558222
With itself (QC-failed)	0	0	0	0
Singletons	0	0	0	0
Singletons (QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0

Filtered and duplicates removed

Sequence quality metrics (filtered/deduped BAM)

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.

Library complexity quality metrics

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1	ctl2
Total Fragments	9686096	8837555	579915	776487
Distinct Fragments	606534	464775	29612	40375
Positions with Two Read	33459	22661	1244	1466
NRF = Distinct/Total	0.062619	0.052591	0.051063	0.051997
PBC1 = OneRead/Distinct	0.162629	0.153567	0.068722	0.065684
PBC2 = OneRead/TwoRead	2.948086	3.14964	1.635852	1.809004

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1. See more details at the ENCODE portal standard for ChIP-Seq pipeline

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

Replication quality metrics

IDR (Irreproducible Discovery Rate) plots

Reproducibility QC and peak detection statistics

	overlap	idr
Nt	1172	336
N1	1310	1070
N2	1270	1001
Np	1264	1087
N optimal	1264	1087
N conservative	1172	336
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0784982935153584	3.2351190476190474
Self Consistency Ratio	1.031496062992126	1.068931068931069
Reproducibility Test	pass	borderline

Reproducibility QC

N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent 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'

Number of raw peaks

	rep1	rep2
Number of peaks	1375	1339

Top 500000 raw peaks from macs2 with p-val threshold 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	150.0	150.0	150.0	150.0
25 percentile	254.5	261.5	336.0	291.75
50 percentile (median)	414.0	410.0	484.0	436.5
75 percentile	629.0	641.5	692.0	654.25
Max size	1755.0	2253.0	2220.0	2220.0
Mean	464.7163636363636	475.7580283793876	527.5630174793008	489.0039556962025

Enrichment / Signal-to-noise ratio

Strand cross-correlation measures (trimmed/filtered SE BAM)

	rep1	rep2
Number of Subsampled Reads	9686096	8837555
Estimated Fragment Length	230	270
Cross-correlation at Estimated Fragment Length	0.603829150645678	0.579541319645705
Phantom Peak	80	80
Cross-correlation at Phantom Peak	0.5475729	0.4974463
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.3468597	0.2859085
NSC (Normalized Strand Cross-correlation coeff.)	1.740845	2.027017
RSC (Relative Strand Cross-correlation coeff.)	1.280282	1.388087

Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50. Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only. Untrimmed FASTQs are used for all the other analyses.

NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.

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

Jensen-Shannon distance (filtered/deduped BAM)

	rep1	rep2
AUC	0.12617500297504713	0.12617500297504713
Synthetic AUC	0.4991465586770113	0.4991465586770113
X-intercept	0.04709469620962787	0.04709469620962787
Synthetic X-intercept	1e-323	1e-323
Elbow Point	0.8967065156006612	0.8967065156006612
Synthetic Elbow Point	0.49989027706496575	0.49989027706496575
JS Distance	0.40377581359660636	0.40377581359660636
Synthetic JS Distance	0.6100023580266389	0.6100023580266389
% Genome Enriched	9.93630652304777	9.93630652304777
Diff. Enrichment	59.23882675847576	59.23882675847576
CHANCE Divergence	0.5330463391578328	0.5330463391578328

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for macs2 raw peaks

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.6338137850368802	0.6667747388897894	0.6345420598659121	0.6670107655737516	0.6341831220868192	0.666809382266634	0.6461705607139169	0.6464848539395602	0.6461601210585661

FRiP for overlap peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.6408424516361854	0.6314399544959988	0.6644975404155283	0.6450456879842767

FRiP for IDR peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.5256088551498929	0.5104286014785503	0.5280827554576002	0.6152981613353778

For macs2 raw peaks:

repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)

For overlap/IDR peaks:

repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates