QC Report

	general
Report generated at	2019-11-26 18:01:48
Title	AWRI1631--CUP9
Description	chipseq of yeast AWRI1631 for tf CUP9
Pipeline version	v1.3.3
Pipeline type	tf
Genome	AWRI1631
Paired-end per replicate	[True, True, True]
Aligner	bowtie2
Peak caller	spp
Control paired-end per replicate	[True, True, True, True]

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	rep3	ctl1	ctl2	ctl3	ctl4
Total Reads	7125354	5742796	5384188	5917546	6601090	11652572	8804978
Total Reads (QC-failed)	0	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0	0
Mapped Reads	5102526	4254827	4641444	4977004	5788309	9693515	6321027
Mapped Reads (QC-failed)	0	0	0	0	0	0	0
% Mapped Reads	71.6	74.1	86.2	84.1	87.7	83.2	71.8
Paired Reads	7125354	5742796	5384188	5917546	6601090	11652572	8804978
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	3562677	2871398	2692094	2958773	3300545	5826286	4402489
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	3562677	2871398	2692094	2958773	3300545	5826286	4402489
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	4229820	3458754	3856444	3717114	4357276	7216522	3826466
Properly Paired Reads (QC-failed)	0	0	0	0	0	0	0
% Properly Paired Reads	59.4	60.199999999999996	71.6	62.8	66.0	61.9	43.5
With itself	5034724	4132104	4539710	4894834	5693772	9527698	5338574
With itself (QC-failed)	0	0	0	0	0	0	0
Singletons	67802	122723	101734	82170	94537	165817	982453
Singletons (QC-failed)	0	0	0	0	0	0	0
% Singleton	1.0	2.1	1.9	1.4000000000000001	1.4000000000000001	1.4000000000000001	11.200000000000001
Diff. Chroms	1283	2184	2497	2445	2633	5103	2765
Diff. Chroms (QC-failed)	0	0	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	rep3	ctl1	ctl2	ctl3	ctl4
Unpaired Reads	0	0	0	0	0	0	0
Paired Reads	1713446	1079882	1112021	1618488	1908814	3134719	1665993
Unmapped Reads	0	0	0	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0	0	0	0
Paired Duplicate Reads	29045	12531	16988	4666	7580	17416	5903
Paired Optical Duplicate Reads	506	312	224	658	501	1171	1570
% Duplicate Reads	1.6951	1.1603999999999999	1.5277	0.2883	0.39709999999999995	0.5556	0.3543

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	rep3	ctl1	ctl2	ctl3	ctl4
Total Reads	3368802	2134702	2190066	3227644	3802468	6234606	3320180
Total Reads (QC-failed)	0	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0	0
Mapped Reads	3368802	2134702	2190066	3227644	3802468	6234606	3320180
Mapped Reads (QC-failed)	0	0	0	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0	100.0	100.0	100.0
Paired Reads	3368802	2134702	2190066	3227644	3802468	6234606	3320180
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	1684401	1067351	1095033	1613822	1901234	3117303	1660090
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	1684401	1067351	1095033	1613822	1901234	3117303	1660090
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	3368802	2134702	2190066	3227644	3802468	6234606	3320180
Properly Paired Reads (QC-failed)	0	0	0	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0	100.0	100.0	100.0
With itself	3368802	2134702	2190066	3227644	3802468	6234606	3320180
With itself (QC-failed)	0	0	0	0	0	0	0
Singletons	0	0	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	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	rep3	ctl1	ctl2	ctl3	ctl4
Total Fragments	1710677	1075099	1110113	1571325	1852755	3044551	1629062
Distinct Fragments	1681740	1062648	1093212	1567386	1846120	3029617	1623881
Positions with Two Read	27502	11901	16241	3865	6528	14432	5101
NRF = Distinct/Total	0.983084	0.988419	0.984775	0.997493	0.996419	0.995095	0.99682
PBC1 = OneRead/Distinct	0.983243	0.988551	0.98485	0.997511	0.996436	0.995157	0.996835
PBC2 = OneRead/TwoRead	60.125045	88.268381	66.2921	404.523674	281.792279	208.906943	317.337973

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	3130	540
N1	3061	735
N2	1831	462
N3	2172	418
Np	3873	682
N optimal	3873	682
N conservative	3130	540
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep2_vs_rep3
Rescue Ratio	1.2373801916932907	1.262962962962963
Self Consistency Ratio	1.6717640633533588	1.7583732057416268
Reproducibility Test	pass	pass

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	rep3
Number of peaks	6978	8301	10008

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	rep3	idr_opt	overlap_opt
Min size	160.0	84.0	80.0	94.0	94.0
25 percentile	640.0	336.0	320.0	293.25	376.0
50 percentile (median)	640.0	336.0	320.0	348.0	376.0
75 percentile	640.0	336.0	320.0	376.0	376.0
Max size	1899.0	726.0	648.0	1424.0	1424.0
Mean	622.0452851820006	333.6382363570654	317.9325539568345	337.6759530791789	368.0526723470178

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	2349029	1372098	1395798
Estimated Fragment Length	70	145	135
Cross-correlation at Estimated Fragment Length	0.878947871494272	0.797658294127845	0.804714723602539
Phantom Peak	50	55	55
Cross-correlation at Phantom Peak	0.8794092	0.7907902	0.7987001
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.8638458	0.7531984	0.7713638
NSC (Normalized Strand Cross-correlation coeff.)	1.017482	1.059028	1.043236
RSC (Relative Strand Cross-correlation coeff.)	0.9703584	1.182703	1.220024

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

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

	rep1	rep2	rep3	rep1-pr1	rep2-pr1	rep3-pr1	rep1-pr2	rep2-pr2	rep3-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.39563411562923556	0.42585335095952503	0.46093816350740113	0.35975378799122776	0.3453209437936126	0.371193953795042	0.3415946331037758	0.3421276994425446	0.35063724165138555	0.29965997579797155	0.35881675829289267	0.3601397219806061

FRiP for overlap peaks

	rep1_vs_rep2	rep1_vs_rep3	rep2_vs_rep3	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.19004792313581342	0.18376111480106114	0.2009264879633252	0.23193883166775608	0.20136534279726162	0.18663821090323304	0.23942669008015785

FRiP for IDR peaks

	rep1_vs_rep2	rep1_vs_rep3	rep2_vs_rep3	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.07367580979961189	0.06718844437627786	0.09165069012175102	0.09355581004760744	0.12653850514029594	0.09889838936360822	0.10408483967780888

For spp 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