The path to the taglign is gs://caper_in/CRC_finemap/tagalign/Enterocytes.tsv.gz
Pipeline version
v1.10.0
Pipeline type
atac
Genome
hg38
Aligner
bowtie2
Sequencing endedness
{'rep1': {'paired_end': True}}
Peak caller
macs2
Alignment quality metrics
Annotated genomic region enrichment
rep1
Fraction of Reads in universal DHS regions
0.5627381836251253
Fraction of Reads in blacklist regions
0.001003150378726064
Fraction of Reads in promoter regions
0.23056904621907273
Fraction of Reads in enhancer regions
0.39193386827427973
Signal to noise can be assessed by considering whether reads are falling into
known open regions (such as DHS regions) or not. A high fraction of reads
should fall into the universal (across cell type) DHS set. A small fraction
should fall into the blacklist regions. A high set (though not all) should
fall into the promoter regions. A high set (though not all) should fall into
the enhancer regions. The promoter regions should not take up all reads, as
it is known that there is a bias for promoters in open chromatin assays.
Replication quality metrics
IDR (Irreproducible Discovery Rate) plots
rep1-pr1_vs_rep1-pr2
Reproducibility QC and peak detection statistics
overlap
idr
Nt
0
0
N1
157235
105340
Np
0
0
N optimal
157235
105340
N conservative
157235
105340
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
203017
Top 300000 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
150.0
150.0
25 percentile
255.0
476.0
355.0
50 percentile (median)
441.0
683.0
556.0
75 percentile
736.0
960.0
831.0
Max size
2850.0
2850.0
2850.0
Mean
542.8593763083879
747.7451775204102
634.8007377492289
rep1idr_optoverlap_opt
Peak enrichment
Fraction of reads in peaks (FRiP)
FRiP for macs2 raw peaks
rep1
rep1-pr1
rep1-pr2
Fraction of Reads in Peaks
0.5077113132084596
0.494963035042497
0.49239222138524213
FRiP for overlap peaks
rep1-pr1_vs_rep1-pr2
Fraction of Reads in Peaks
0.48991645185914484
FRiP for IDR peaks
rep1-pr1_vs_rep1-pr2
Fraction of Reads in Peaks
0.4500975069923676
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
