QC Report

	general
Report generated at	2019-11-28 09:24:02
Title	YJM789--RPD3
Description	chipseq of yeast YJM789 for tf RPD3
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	5510822	4214164	8692632	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	4874015	3911893	7568134	3915768	5764661	8424118	5371312
Mapped Reads (QC-failed)	0	0	0	0	0	0	0
% Mapped Reads	88.4	92.80000000000001	87.1	78.0	77.8	76.2	64.1
Paired Reads	5510822	4214164	8692632	5022862	7410926	11061052	8381776
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	2755411	2107082	4346316	2511431	3705463	5530526	4190888
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	2755411	2107082	4346316	2511431	3705463	5530526	4190888
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	4247470	3668766	6579638	2796040	4317758	6012756	3063152
Properly Paired Reads (QC-failed)	0	0	0	0	0	0	0
% Properly Paired Reads	77.10000000000001	87.1	75.7	55.7	58.3	54.400000000000006	36.5
With itself	4822620	3886612	7480330	3839630	5654854	8256416	4415930
With itself (QC-failed)	0	0	0	0	0	0	0
Singletons	51395	25281	87804	76138	109807	167702	955382
Singletons (QC-failed)	0	0	0	0	0	0	0
% Singleton	0.8999999999999999	0.6	1.0	1.5	1.5	1.5	11.4
Diff. Chroms	2042	1834	3207	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	1844517	1623833	2850487	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	19377	12203	51101	3005	7226	12971	4196
Paired Optical Duplicate Reads	779	765	1168	517	518	966	1248
% Duplicate Reads	1.0505	0.7515	1.7927	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	3650280	3223260	5598772	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	3650280	3223260	5598772	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	3650280	3223260	5598772	2459064	3796058	5259790	2693488
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	1825140	1611630	2799386	1229532	1898029	2629895	1346744
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	1825140	1611630	2799386	1229532	1898029	2629895	1346744
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	3650280	3223260	5598772	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	3650280	3223260	5598772	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	1841196	1622117	2845678	1191364	1836406	2555651	1314860
Distinct Fragments	1821875	1609933	2794717	1188897	1830268	2544930	1311276
Positions with Two Read	18947	12016	48845	2445	6088	10557	3566
NRF = Distinct/Total	0.989506	0.992489	0.982092	0.997929	0.996658	0.995805	0.997274
PBC1 = OneRead/Distinct	0.989498	0.992485	0.98215	0.997934	0.99666	0.99582	0.997274
PBC2 = OneRead/TwoRead	95.146567	132.975533	56.194718	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	4043	914
N1	4132	824
N2	3404	728
N3	4644	899
Np	4225	1053
N optimal	4225	1053
N conservative	4043	914
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep3	rep1_vs_rep3
Rescue Ratio	1.045016077170418	1.1520787746170678
Self Consistency Ratio	1.36427732079906	1.23489010989011
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	7670	7405	6702

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	112.0	121.0	129.0	129.0
25 percentile	460.0	450.0	484.0	310.0	516.0
50 percentile (median)	460.0	450.0	484.0	516.0	516.0
75 percentile	460.0	450.0	484.0	516.0	516.0
Max size	1314.0	902.0	2050.0	2139.0	2139.0
Mean	450.8089960886571	441.3594868332208	472.83318412414206	493.13675213675214	506.72213017751477

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	2212087	1716189	3427731
Estimated Fragment Length	140	160	130
Cross-correlation at Estimated Fragment Length	0.874280866757628	0.846062461676197	0.912225093939748
Phantom Peak	50	50	50
Cross-correlation at Phantom Peak	0.875397	0.8457382	0.9134619
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.8615458	0.8337028	0.8994796
NSC (Normalized Strand Cross-correlation coeff.)	1.014782	1.014825	1.01417
RSC (Relative Strand Cross-correlation coeff.)	0.9194215	1.026943	0.9115451

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	0.3790350329289808	0.3757819722889249	0.33992596948045034	0.4060269349200609	0.3757915898810521	0.4066931105606729	0.4122067348258216	0.3724328785142992	0.4039064280524372	0.2870968109200604	0.3293540123114303	0.3309065712916739

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	0.23397009311505357	0.24574248944381763	0.23760694889608278	0.25875330111662664	0.22851833237157412	0.27278321031826264	0.25168284757469184

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	0.0872980085809271	0.09651698899129528	0.09267816584447214	0.08583505922833316	0.07675707203266259	0.0929325216315292	0.10669882215903514

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