QC Report

	general
Report generated at	2021-06-18 04:57:08
Title	runx1_k562_1
Description	chipseq of runx1_k562_1
Pipeline version	v1.3.6
Pipeline type	tf
Genome	hg38
Aligner	bowtie2
Sequencing endedness	{'rep1': {'paired_end': True}, 'rep2': {'paired_end': True}, 'ctl1': {'paired_end': True}, 'ctl2': {'paired_end': True}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2
Total Reads	70652304	65136808	90517746	95213346
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	69333266	63748098	89458661	94154887
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	98.1	97.89999999999999	98.8	98.9
Paired Reads	70652304	65136808	90517746	95213346
Paired Reads (QC-failed)	0	0	0	0
Read1	35326152	32568404	45258873	47606673
Read1 (QC-failed)	0	0	0	0
Read2	35326152	32568404	45258873	47606673
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	68889794	63362488	88889944	93535642
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	97.5	97.3	98.2	98.2
With itself	68989440	63421190	89037122	93722754
With itself (QC-failed)	0	0	0	0
Singletons	343826	326908	421539	432133
Singletons (QC-failed)	0	0	0	0
% Singleton	0.5	0.5	0.5	0.5
Diff. Chroms	15519	10777	38020	40990
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2
Unpaired Reads	0	0	0	0
Paired Reads	29636001	27302893	37410880	39565402
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0
Paired Duplicate Reads	2643831	6667719	2744207	2210699
Paired Optical Duplicate Reads	0	0	0	0
% Duplicate Reads	8.921	24.421300000000002	7.3353	5.5875

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
Total Reads	53984340	41270348	69333346	74709406
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	53984340	41270348	69333346	74709406
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0
Paired Reads	53984340	41270348	69333346	74709406
Paired Reads (QC-failed)	0	0	0	0
Read1	26992170	20635174	34666673	37354703
Read1 (QC-failed)	0	0	0	0
Read2	26992170	20635174	34666673	37354703
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	53984340	41270348	69333346	74709406
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0
With itself	53984340	41270348	69333346	74709406
With itself (QC-failed)	0	0	0	0
Singletons	0	0	0	0
Singletons (QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	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
Total Fragments	29581115	27224300	36686094	38983260
Distinct Fragments	26943714	20577690	34174655	36939155
Positions with Two Read	2242507	4128645	2235543	1866995
NRF = Distinct/Total	0.910842	0.755857	0.931542	0.947565
PBC1 = OneRead/Distinct	0.909724	0.744518	0.930658	0.947118
PBC2 = OneRead/TwoRead	10.930332	3.71077	14.226924	18.739069

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	19760	1989
N1	21369	1288
N2	13070	877
Np	19865	2263
N optimal	19865	2263
N conservative	19760	1989
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0053137651821862	1.1377576671694318
Self Consistency Ratio	1.634965570007651	1.468643101482326
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	179804	171003

Top 500000 raw peaks from macs2 with p-val threshold 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	175.0	180.0	178.0	178.0
25 percentile	188.0	187.0	311.0	284.0
50 percentile (median)	230.0	225.0	392.0	357.0
75 percentile	300.0	291.0	525.0	470.0
Max size	2069.0	1342.0	1925.0	1925.0
Mean	262.3556817423417	254.51796752103763	448.44896155545734	400.49061162849233

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	15000000	15000000
Estimated Fragment Length	175	180
Cross-correlation at Estimated Fragment Length	0.166958806804756	0.143842922054741
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.1655035	0.1392211
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.1614896	0.136044
NSC (Normalized Strand Cross-correlation coeff.)	1.033867	1.057326
RSC (Relative Strand Cross-correlation coeff.)	1.362565	2.454725

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

Jensen-Shannon distance (filtered/deduped BAM)

	rep1	rep2
AUC	0.26657546249466435	0.25990532473534045
Synthetic AUC	0.49522810361408276	0.4945366714076587
X-intercept	0.13219478938203136	0.1481213425008647
Synthetic X-intercept	0.0	1.2364329744946279e-287
Elbow Point	0.5882428209552333	0.5858936243804619
Synthetic Elbow Point	0.5016704898505153	0.5082236724145428
JS Distance	0.06973843023378799	0.062281010836744845
Synthetic JS Distance	0.2879086489881233	0.2895408187619467
% Genome Enriched	39.80478676292708	39.06803873075408
Diff. Enrichment	12.083533077564596	14.043727081501778
CHANCE Divergence	0.10920839427399888	0.1265187329369048

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for macs2 raw peaks

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.08224505476958688	0.07948845015796814	0.0933894533118308	0.08176107456132911	0.09392234859220285	0.08178559579870759	0.06588681493555466	0.06617553563347979	0.06637787738069123

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	0.015878399601707793	0.017812554529702502	0.01183464699643434	0.016742892486299468

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	0.003907891651484911	0.0029597657394718545	0.002181178603097798	0.0043270311273288726

For macs2 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