QC Report

	general
Report generated at	2019-12-04 05:34:47
Title	BY4741--CUP2
Description	chipseq of yeast BY4741 for tf CUP2
Pipeline version	v1.3.3
Pipeline type	tf
Genome	BY4741
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	5708628	6048982	7838426	3821096	6022122	7681960	6051150
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	4262056	4836006	688682	3637548	5765508	7297990	5604692
Mapped Reads (QC-failed)	0	0	0	0	0	0	0
% Mapped Reads	74.7	79.9	8.799999999999999	95.19999999999999	95.7	95.0	92.60000000000001
Paired Reads	5708628	6048982	7838426	3821096	6022122	7681960	6051150
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	2854314	3024491	3919213	1910548	3011061	3840980	3025575
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	2854314	3024491	3919213	1910548	3011061	3840980	3025575
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	3683294	3979600	539750	3465580	4596636	6940440	4773966
Properly Paired Reads (QC-failed)	0	0	0	0	0	0	0
% Properly Paired Reads	64.5	65.8	6.9	90.7	76.3	90.3	78.9
With itself	4221330	4701136	667494	3614474	5715646	7250214	5436122
With itself (QC-failed)	0	0	0	0	0	0	0
Singletons	40726	134870	21188	23074	49862	47776	168570
Singletons (QC-failed)	0	0	0	0	0	0	0
% Singleton	0.7000000000000001	2.1999999999999997	0.3	0.6	0.8	0.6	2.8000000000000003
Diff. Chroms	917	3461	896	5037	2033	9551	4281
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	1553670	1290177	148648	1416051	1965291	2814559	1975211
Unmapped Reads	0	0	0	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0	0	0	0
Paired Duplicate Reads	28285	14013	667	3676	6905	14229	6671
Paired Optical Duplicate Reads	510	346	56	610	543	1167	1986
% Duplicate Reads	1.8205	1.0861	0.4487	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	rep3	ctl1	ctl2	ctl3	ctl4
Total Reads	3050770	2552328	295962	2824750	3916772	5600660	3937080
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	3050770	2552328	295962	2824750	3916772	5600660	3937080
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	3050770	2552328	295962	2824750	3916772	5600660	3937080
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	1525385	1276164	147981	1412375	1958386	2800330	1968540
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	1525385	1276164	147981	1412375	1958386	2800330	1968540
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	3050770	2552328	295962	2824750	3916772	5600660	3937080
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	3050770	2552328	295962	2824750	3916772	5600660	3937080
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	1550045	1285221	148257	1405680	1919660	2794172	1964730
Distinct Fragments	1521873	1271300	147594	1402051	1913239	2780126	1958152
Positions with Two Read	27167	13223	653	3498	6284	13066	6370
NRF = Distinct/Total	0.981825	0.989168	0.995528	0.997418	0.996655	0.994973	0.996652
PBC1 = OneRead/Distinct	0.981824	0.989338	0.995542	0.997461	0.99668	0.995139	0.996695
PBC2 = OneRead/TwoRead	55.000957	95.117976	225.016845	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	2945	532
N1	5622	560
N2	3360	492
N3	1424	521
Np	3637	712
N optimal	3637	712
N conservative	2945	532
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.234974533106961	1.3383458646616542
Self Consistency Ratio	3.9480337078651684	1.1382113821138211
Reproducibility Test	borderline	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	8226	5665	6387

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	81.0	85.0	80.0	89.0	89.0
25 percentile	324.0	340.0	320.0	294.75	356.0
50 percentile (median)	324.0	340.0	320.0	356.0	356.0
75 percentile	324.0	340.0	320.0	356.0	356.0
Max size	413.0	762.0	424.0	912.0	912.0
Mean	321.02577194262096	337.166107678729	314.6801315171442	326.8637640449438	348.5523783337916

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	1912148	1666050	212414
Estimated Fragment Length	135	145	95
Cross-correlation at Estimated Fragment Length	0.857224581394228	0.825078880058423	0.453790337395506
Phantom Peak	50	55	55
Cross-correlation at Phantom Peak	0.8563823	0.8128848	0.4396582
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.848858	0.7709688	0.3319049
NSC (Normalized Strand Cross-correlation coeff.)	1.009856	1.070184	1.36723
RSC (Relative Strand Cross-correlation coeff.)	1.111943	1.290918	1.131153

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	0.31830259246026416	0.33566884820446274	0.4733479298017989	0.38968169368277933	0.383580793691093	0.475834898839048	0.38285244895711507	0.38331123585996785	0.4793215299364779	0.24262492668323427	0.29026774417093965	0.28873094271354605

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	0.16414581306174203	0.11048878973938221	0.13082525012459612	0.2388777259511533	0.2654086778815262	0.23709124820078253	0.2069007604601411

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	0.06846514529433503	0.05521066068153231	0.08478605065891855	0.04133776063092268	0.14304313552176678	0.1747183760077307	0.0967988120141175

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