QC Report

	general
Report generated at	2019-11-21 16:12:32
Title	YJM789--MAC1
Description	chipseq of yeast YJM789 for tf MAC1
Pipeline version	v1.3.3
Pipeline type	tf
Genome	YJM789
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	4991604	8158162	4393626	5022862	7410926	11061052	8381776
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	3811739	6097599	3790488	3915768	5764661	8424118	5371312
Mapped Reads (QC-failed)	0	0	0	0	0	0	0
% Mapped Reads	76.4	74.7	86.3	78.0	77.8	76.2	64.1
Paired Reads	4991604	8158162	4393626	5022862	7410926	11061052	8381776
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	2495802	4079081	2196813	2511431	3705463	5530526	4190888
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	2495802	4079081	2196813	2511431	3705463	5530526	4190888
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	3379192	5132326	3125056	2796040	4317758	6012756	3063152
Properly Paired Reads (QC-failed)	0	0	0	0	0	0	0
% Properly Paired Reads	67.7	62.9	71.1	55.7	58.3	54.400000000000006	36.5
With itself	3739904	5951728	3695536	3839630	5654854	8256416	4415930
With itself (QC-failed)	0	0	0	0	0	0	0
Singletons	71835	145871	94952	76138	109807	167702	955382
Singletons (QC-failed)	0	0	0	0	0	0	0
% Singleton	1.4000000000000001	1.7999999999999998	2.1999999999999997	1.5	1.5	1.5	11.4
Diff. Chroms	2141	3718	2421	1527	2704	3477	1976
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	1323414	2119982	1167457	1232537	1905255	2642866	1350940
Unmapped Reads	0	0	0	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0	0	0	0
Paired Duplicate Reads	52314	52368	8764	3005	7226	12971	4196
Paired Optical Duplicate Reads	419	646	258	517	518	966	1248
% Duplicate Reads	3.9530000000000003	2.4702	0.7506999999999999	0.24380000000000002	0.37929999999999997	0.4908	0.3106

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	2542200	4135228	2317386	2459064	3796058	5259790	2693488
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	2542200	4135228	2317386	2459064	3796058	5259790	2693488
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	2542200	4135228	2317386	2459064	3796058	5259790	2693488
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	1271100	2067614	1158693	1229532	1898029	2629895	1346744
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	1271100	2067614	1158693	1229532	1898029	2629895	1346744
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	2542200	4135228	2317386	2459064	3796058	5259790	2693488
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	2542200	4135228	2317386	2459064	3796058	5259790	2693488
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	1320191	2109455	1163919	1191364	1836406	2555651	1314860
Distinct Fragments	1268065	2057473	1155229	1188897	1830268	2544930	1311276
Positions with Two Read	48761	49552	8516	2445	6088	10557	3566
NRF = Distinct/Total	0.960516	0.975358	0.992534	0.997929	0.996658	0.995805	0.997274
PBC1 = OneRead/Distinct	0.960247	0.975335	0.992555	0.997934	0.99666	0.99582	0.997274
PBC2 = OneRead/TwoRead	24.971924	40.497356	134.643964	485.251943	299.631242	240.057971	366.713685

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	4034	661
N1	3143	625
N2	2158	541
N3	3620	431
Np	5059	691
N optimal	5059	691
N conservative	4034	661
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep2_vs_rep3	rep1_vs_rep2
Rescue Ratio	1.2540902330193358	1.0453857791225416
Self Consistency Ratio	1.6774791473586654	1.4501160092807424
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	9575	8934	11385

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	91.0	91.0	94.0	93.0	93.0
25 percentile	364.0	364.0	304.0	311.0	370.0
50 percentile (median)	364.0	364.0	304.0	361.0	370.0
75 percentile	364.0	364.0	304.0	370.0	370.0
Max size	732.0	696.0	470.0	718.0	718.0
Mean	359.1205221932115	360.57062905753304	301.46262626262626	335.90593342981185	364.89503854516704

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	1476968	2628966	1485961
Estimated Fragment Length	180	135	135
Cross-correlation at Estimated Fragment Length	0.814974172111208	0.875860623556498	0.813018522156367
Phantom Peak	50	50	55
Cross-correlation at Phantom Peak	0.8123085	0.8760212	0.8079943
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.7980712	0.8559943	0.7868233
NSC (Normalized Strand Cross-correlation coeff.)	1.02118	1.023209	1.033292
RSC (Relative Strand Cross-correlation coeff.)	1.187232	0.9919841	1.237315

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	0.4423062701597042	0.41225272221991144	0.4879247566007562	0.3895586499881992	0.3115233307570949	0.43323517684565555	0.3905231689088191	0.31594872156988685	0.4584143154522513	0.358575730415326	0.41739642033811475	0.41689342701103704

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	0.22913625562462991	0.23089171160181857	0.23944886464578366	0.21294430021241445	0.18464205601238917	0.2283408978909858	0.27888014137924366

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	0.10245436981798622	0.09695686870234337	0.09676998323700746	0.08286130123515066	0.10239798144141024	0.08750721718349899	0.10447620150900286

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