QC Report

	general
Report generated at	2021-06-26 15:48:03
Title	15402_ELK1_K562-8M
Description	chipexo of 15402_ELK1_K562-8M
Pipeline version	v1.3.6
Pipeline type	tf
Genome	hg38
Aligner	bowtie2
Sequencing endedness	{'rep1': {'paired_end': True}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1
Total Reads	10359242
Total Reads (QC-failed)	0
Duplicate Reads	0
Duplicate Reads (QC-failed)	0
Mapped Reads	7743010
Mapped Reads (QC-failed)	0
% Mapped Reads	74.7
Paired Reads	10359242
Paired Reads (QC-failed)	0
Read1	5179621
Read1 (QC-failed)	0
Read2	5179621
Read2 (QC-failed)	0
Properly Paired Reads	6490946
Properly Paired Reads (QC-failed)	0
% Properly Paired Reads	62.7
With itself	7067272
With itself (QC-failed)	0
Singletons	675738
Singletons (QC-failed)	0
% Singleton	6.5
Diff. Chroms	223836
Diff. Chroms (QC-failed)	0

Marking duplicates (filtered BAM)

	rep1
Unpaired Reads	0
Paired Reads	2754804
Unmapped Reads	0
Unpaired Duplicate Reads	0
Paired Duplicate Reads	1683824
Paired Optical Duplicate Reads	0
% Duplicate Reads	61.1232

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
Total Reads	2141960
Total Reads (QC-failed)	0
Duplicate Reads	0
Duplicate Reads (QC-failed)	0
Mapped Reads	2141960
Mapped Reads (QC-failed)	0
% Mapped Reads	100.0
Paired Reads	2141960
Paired Reads (QC-failed)	0
Read1	1070980
Read1 (QC-failed)	0
Read2	1070980
Read2 (QC-failed)	0
Properly Paired Reads	2141960
Properly Paired Reads (QC-failed)	0
% Properly Paired Reads	100.0
With itself	2141960
With itself (QC-failed)	0
Singletons	0
Singletons (QC-failed)	0
% Singleton	0.0
Diff. Chroms	0
Diff. Chroms (QC-failed)	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
Total Fragments	2690145
Distinct Fragments	1044468
Positions with Two Read	261220
NRF = Distinct/Total	0.388257
PBC1 = OneRead/Distinct	0.339829
PBC2 = OneRead/TwoRead	1.358782

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	0	0
N1	30058	11
Np	0	0
N optimal	30058	11
N conservative	30058	11
Optimal Set	rep1-pr1_vs_rep1-pr2	rep1-pr1_vs_rep1-pr2
Conservative Set	rep1-pr1_vs_rep1-pr2	rep1-pr1_vs_rep1-pr2
Rescue Ratio	0.0	0.0
Self Consistency Ratio	1.0	1.0
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
Number of peaks	499164

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

Peak calling statistics

Peak region size

	rep1	idr_opt	overlap_opt
Min size	150.0	187.0	150.0
25 percentile	169.0	221.0	185.0
50 percentile (median)	197.0	382.0	242.0
75 percentile	236.0	448.5	323.0
Max size	903.0	488.0	903.0
Mean	209.37940035739757	341.8181818181818	265.1344068134939

Enrichment / Signal-to-noise ratio

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

	rep1
Number of Subsampled Reads	2808538
Estimated Fragment Length	70
Cross-correlation at Estimated Fragment Length	0.0117081351417293
Phantom Peak	40
Cross-correlation at Phantom Peak	0.01301148
Argmin of Cross-correlation	1500
Minimum of Cross-correlation	0.01063119
NSC (Normalized Strand Cross-correlation coeff.)	1.1013
RSC (Relative Strand Cross-correlation coeff.)	0.4524423

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
AUC	0.07116355027622139
Synthetic AUC	0.4610055656851765
X-intercept	0.8009520839081425
Synthetic X-intercept	2.6035521464405436e-05
Elbow Point	0.8075318994093961
Synthetic Elbow Point	0.5499707702465906
Synthetic JS Distance	0.16315146561000748

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for macs2 raw peaks

	rep1	rep1-pr1	rep1-pr2
Fraction of Reads in Peaks	0.5326425330071524	0.8322863172048031	0.8319399055071056

FRiP for overlap peaks

	rep1-pr1_vs_rep1-pr2
Fraction of Reads in Peaks	0.05694317354198958

FRiP for IDR peaks

	rep1-pr1_vs_rep1-pr2
Fraction of Reads in Peaks	0.00024743692692674

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