QC Report

	general
Report generated at	2019-11-21 02:02:12
Title	BY4741--SWI1
Description	chipseq of yeast BY4741 for tf SWI1
Pipeline version	v1.3.3
Pipeline type	tf
Genome	BY4741
Paired-end per replicate	[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	ctl1	ctl2	ctl3	ctl4
Total Reads	1327170	2463098	3821096	6022122	7681960	6051150
Total Reads (QC-failed)	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0
Mapped Reads	1049833	2266570	3637548	5765508	7297990	5604692
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	79.10000000000001	92.0	95.19999999999999	95.7	95.0	92.60000000000001
Paired Reads	1327170	2463098	3821096	6022122	7681960	6051150
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	663585	1231549	1910548	3011061	3840980	3025575
Read1 (QC-failed)	0	0	0	0	0	0
Read2	663585	1231549	1910548	3011061	3840980	3025575
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	727682	2194910	3465580	4596636	6940440	4773966
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	54.800000000000004	89.1	90.7	76.3	90.3	78.9
With itself	1025692	2230782	3614474	5715646	7250214	5436122
With itself (QC-failed)	0	0	0	0	0	0
Singletons	24141	35788	23074	49862	47776	168570
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	1.7999999999999998	1.5	0.6	0.8	0.6	2.8000000000000003
Diff. Chroms	375	1646	5037	2033	9551	4281
Diff. Chroms (QC-failed)	0	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4
Unpaired Reads	0	0	0	0	0	0
Paired Reads	234518	785245	1416051	1965291	2814559	1975211
Unmapped Reads	0	0	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0	0	0
Paired Duplicate Reads	1094	6136	3676	6905	14229	6671
Paired Optical Duplicate Reads	31	298	610	543	1167	1986
% Duplicate Reads	0.46649999999999997	0.7814	0.2596	0.3513	0.5055	0.3377

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	ctl3	ctl4
Total Reads	466848	1558218	2824750	3916772	5600660	3937080
Total Reads (QC-failed)	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0
Mapped Reads	466848	1558218	2824750	3916772	5600660	3937080
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0	100.0	100.0
Paired Reads	466848	1558218	2824750	3916772	5600660	3937080
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	233424	779109	1412375	1958386	2800330	1968540
Read1 (QC-failed)	0	0	0	0	0	0
Read2	233424	779109	1412375	1958386	2800330	1968540
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	466848	1558218	2824750	3916772	5600660	3937080
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0	100.0	100.0
With itself	466848	1558218	2824750	3916772	5600660	3937080
With itself (QC-failed)	0	0	0	0	0	0
Singletons	0	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0	0
Diff. Chroms (QC-failed)	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	ctl1	ctl2	ctl3	ctl4
Total Fragments	233410	778258	1405680	1919660	2794172	1964730
Distinct Fragments	232326	772173	1402051	1913239	2780126	1958152
Positions with Two Read	1061	5857	3498	6284	13066	6370
NRF = Distinct/Total	0.995356	0.992181	0.997418	0.996655	0.994973	0.996652
PBC1 = OneRead/Distinct	0.995386	0.99227	0.997461	0.99668	0.995139	0.996695
PBC2 = OneRead/TwoRead	217.95853	130.818508	399.797313	303.451305	211.741237	306.386342

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	3878	929
N1	2436	679
N2	4109	849
Np	4194	908
N optimal	4194	929
N conservative	3878	929
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0814853017019082	1.0231277533039647
Self Consistency Ratio	1.6867816091954022	1.2503681885125184
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
Number of peaks	6328	6596

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	74.0	106.0	111.0	108.0
25 percentile	296.0	424.0	359.0	430.0
50 percentile (median)	296.0	424.0	430.0	430.0
75 percentile	296.0	424.0	495.0	430.0
Max size	376.0	1445.0	1456.0	1456.0
Mean	288.8119469026549	422.87113402061857	422.43057050592034	425.17405817835004

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	317658	775355
Estimated Fragment Length	130	195
Cross-correlation at Estimated Fragment Length	0.529804396049045	0.687302682042461
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.5068283	0.6313662
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.4164118	0.5750954
NSC (Normalized Strand Cross-correlation coeff.)	1.272309	1.195111
RSC (Relative Strand Cross-correlation coeff.)	1.254114	1.994058

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	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.43889874220302966	0.48700438577914	0.47576084721365414	0.5254457008638062	0.48130440743025565	0.5189550100884601	0.4577584137998465	0.49097709311489784	0.49066301114433913

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	0.38492325682224676	0.283357752416204	0.413062870535445	0.40087384806223597

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	0.26195837567763225	0.18629832407978614	0.2713586930711877	0.2619924486411801

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