QC Report

	general
Report generated at	2019-11-26 14:27:59
Title	BY4742--RPD3
Description	chipseq of yeast BY4742 for tf RPD3
Pipeline version	v1.3.3
Pipeline type	tf
Genome	BY4742
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	3941598	3177752	6416440	4555882	6930446	9302162	7321170
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	3152690	2956219	4973495	4209856	6142696	8516629	6004918
Mapped Reads (QC-failed)	0	0	0	0	0	0	0
% Mapped Reads	80.0	93.0	77.5	92.4	88.6	91.60000000000001	82.0
Paired Reads	3941598	3177752	6416440	4555882	6930446	9302162	7321170
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	1970799	1588876	3208220	2277941	3465223	4651081	3660585
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	1970799	1588876	3208220	2277941	3465223	4651081	3660585
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	2674022	2630248	4215960	3408530	4817860	6865532	4002636
Properly Paired Reads (QC-failed)	0	0	0	0	0	0	0
% Properly Paired Reads	67.80000000000001	82.8	65.7	74.8	69.5	73.8	54.7
With itself	3120898	2940510	4917712	4169336	6059104	8426516	5323690
With itself (QC-failed)	0	0	0	0	0	0	0
Singletons	31792	15709	55783	40520	83592	90113	681228
Singletons (QC-failed)	0	0	0	0	0	0	0
% Singleton	0.8	0.5	0.8999999999999999	0.8999999999999999	1.2	1.0	9.3
Diff. Chroms	692	770	1114	1815	2127	4171	2235
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	1173221	1152087	1842251	1476158	2070343	2961014	1730516
Unmapped Reads	0	0	0	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0	0	0	0
Paired Duplicate Reads	8192	8717	21984	3321	7880	13554	5282
Paired Optical Duplicate Reads	478	497	687	552	549	1092	1711
% Duplicate Reads	0.6982	0.7565999999999999	1.1932999999999998	0.22499999999999998	0.3806	0.45770000000000005	0.3052

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	2330058	2286740	3640534	2945674	4124926	5894920	3450468
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	2330058	2286740	3640534	2945674	4124926	5894920	3450468
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	2330058	2286740	3640534	2945674	4124926	5894920	3450468
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	1165029	1143370	1820267	1472837	2062463	2947460	1725234
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	1165029	1143370	1820267	1472837	2062463	2947460	1725234
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	2330058	2286740	3640534	2945674	4124926	5894920	3450468
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	2330058	2286740	3640534	2945674	4124926	5894920	3450468
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	1171798	1150912	1840042	1449951	2021943	2908895	1705713
Distinct Fragments	1163640	1142223	1818134	1446811	2014504	2895991	1700692
Positions with Two Read	8018	8557	21382	3114	7276	12643	4962
NRF = Distinct/Total	0.993038	0.99245	0.988094	0.997834	0.996321	0.995564	0.997056
PBC1 = OneRead/Distinct	0.993051	0.992451	0.988095	0.997839	0.996349	0.99559	0.997065
PBC2 = OneRead/TwoRead	144.11998	132.476335	84.018801	463.61079	275.858988	228.048723	341.737404

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	2911	911
N1	2450	780
N2	2456	809
N3	2743	917
Np	3196	1025
N optimal	3196	1025
N conservative	2911	911
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep3	rep1_vs_rep3
Rescue Ratio	1.0979045001717622	1.1251372118551042
Self Consistency Ratio	1.119591836734694	1.1756410256410257
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	5224	5004	5147

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	115.0	121.0	119.0	131.0	131.0
25 percentile	460.0	484.0	476.0	329.0	524.0
50 percentile (median)	460.0	484.0	476.0	456.0	524.0
75 percentile	460.0	484.0	476.0	524.0	524.0
Max size	1396.0	1242.0	1868.0	3848.0	3848.0
Mean	445.1447166921899	466.6193045563549	459.74392850204003	526.6039024390244	516.5588235294117

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	1486594	1307306	2340493
Estimated Fragment Length	135	160	140
Cross-correlation at Estimated Fragment Length	0.828664917339417	0.810832352443812	0.881489859856919
Phantom Peak	55	55	55
Cross-correlation at Phantom Peak	0.8258529	0.8073032	0.878939
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.8088682	0.7918369	0.8603739
NSC (Normalized Strand Cross-correlation coeff.)	1.024475	1.023989	1.024543
RSC (Relative Strand Cross-correlation coeff.)	1.165563	1.228182	1.137398

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	0.322400558269365	0.32120267280058074	0.30895522470055214	0.3238079706101989	0.3322668952307652	0.3099021682521475	0.33777643112440214	0.3366819139910965	0.3246717787400303	0.262607098757807	0.301449038769889	0.3011419674742241

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	0.20935769568184978	0.221360604127338	0.21560947289027496	0.20636524927705663	0.20967928142246167	0.21891266501013312	0.23203560181424218

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	0.10889037766678147	0.11434407627064044	0.11479519050463273	0.09836450423122514	0.1008265041062823	0.11299743389293988	0.12411454450420548

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