ExperimentSetReplicate

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ExperimentSet4DNESAZRVEQ8
released
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Replicates of dilution Hi-C on GM18505

   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 
GM18505
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
4DNESAZRVEQ8
Multiple Experiments
File
4DNFI67T52AI
contact list-combined (pairs)
6.56 GB
-
File
4DNFIF9BDCNI
contact matrix (hic)
3.57 GB
-
File
4DNFIIDNWL5I
contact matrix (mcool)
2.33 GB
File
4DNFICIIRUNS
boundaries (bed)
149.78 kB
-
File
4DNFIKWGCCD9
insulation score-diamond (bw)
3.95 MB
-
File
4DNFI41N8FVG
compartments (bw)
205.03 kB
-
Experiment
4DNEXLEHFN7H
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM18505 with HindIII
File
4DNFI1YGP8NI
alignments (bam)
48.36 GB
-
File
4DNFIZ5I4WHB
contact list-replicate (pairs)
2.7 GB
-
Experiment
4DNEXCQG4BRQ
Bio Rep 2, Tec Rep 1
Dilution Hi-C on GM18505 with HindIII
File
4DNFIT2X1PMM
alignments (bam)
82.34 GB
-
File
4DNFI8MJRZJ4
contact list-replicate (pairs)
4.3 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESAZRVEQ8
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI67T52AI
356.06m
37.398%
29.026%
33.575%
Experiment
4DNEXLEHFN7H
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM18505 with HindIII
File
Contact List-replicate (pairs)
4DNFIZ5I4WHB
139.26m
27.252%
34.955%
37.793%
Experiment
4DNEXCQG4BRQ
Bio Rep 2, Tec Rep 1
Dilution Hi-C on GM18505 with HindIII
File
Contact List-replicate (pairs)
4DNFI8MJRZJ4
216.81m
43.915%
25.218%
30.866%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESAZRVEQ8
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIIDNWL5I
1000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXLEHFN7H
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM18505 with HindIII
File
Alignments (bam)
4DNFI1YGP8NI
220.5m
16.14%
8.391%
7.387%
4.925%
0.366%
Experiment
4DNEXCQG4BRQ
Bio Rep 2, Tec Rep 1
Dilution Hi-C on GM18505 with HindIII
File
Alignments (bam)
4DNFIT2X1PMM
341.84m
12.268%
7.731%
11.096%
5.482%
0.393%