ExperimentSetReplicate

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ExperimentSet4DNESG9UPQLY
released
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Replicates of dilution Hi-C on GM19193

   March 29th, 2019 at 10:51pm
Source Publication
Common DNA sequence variation influences 3-dimensional conformation of the human genome.
Gorkin DU, Qiu Y, et al., Genome biology 2019

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
GM19193
Experiment Type(s) 
Dilution Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: HindIII

10 Processed Files

    Explore Data

Loading
Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNESG9UPQLY
Multiple Experiments
File
4DNFICET1YND
contact list-combined (pairs)
5.27 GB
-
File
4DNFINHT8P7C
contact matrix (hic)
3.07 GB
-
File
4DNFIPC3LHWT
contact matrix (mcool)
1.99 GB
File
4DNFIYJTPB3V
boundaries (bed)
158.99 kB
-
File
4DNFI71Q11X9
insulation score-diamond (bw)
3.93 MB
-
File
4DNFIHHVPT6G
compartments (bw)
205.03 kB
-
Experiment
4DNEXZ1JAG6F
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM19193 with HindIII
File
4DNFI2CT1P95
alignments (bam)
48.34 GB
-
File
4DNFIUK5FXHG
contact list-replicate (pairs)
2.78 GB
-
Experiment
4DNEX9XWW3E8
Bio Rep 2, Tec Rep 1
Dilution Hi-C on GM19193 with HindIII
File
4DNFIOB6R2EM
alignments (bam)
43.62 GB
-
File
4DNFIINPP7IU
contact list-replicate (pairs)
2.82 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESG9UPQLY
Multiple Experiments
File
Contact List-combined (pairs)
4DNFICET1YND
287.13m
39.454%
27.665%
32.881%
Experiment
4DNEXZ1JAG6F
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM19193 with HindIII
File
Contact List-replicate (pairs)
4DNFIUK5FXHG
142.21m
36.881%
26.896%
36.223%
Experiment
4DNEX9XWW3E8
Bio Rep 2, Tec Rep 1
Dilution Hi-C on GM19193 with HindIII
File
Contact List-replicate (pairs)
4DNFIINPP7IU
144.93m
41.979%
28.42%
29.601%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESG9UPQLY
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIPC3LHWT
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXZ1JAG6F
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM19193 with HindIII
File
Alignments (bam)
4DNFI2CT1P95
219.63m
15.611%
8.074%
7.055%
4.51%
0.291%
Experiment
4DNEX9XWW3E8
Bio Rep 2, Tec Rep 1
Dilution Hi-C on GM19193 with HindIII
File
Alignments (bam)
4DNFIOB6R2EM
209.95m
12.253%
8.049%
6.996%
3.67%
0.351%