ExperimentSetReplicate

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ExperimentSet4DNES3IV77UJ
released
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Replicates of dilution Hi-C on GM18516

   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 
GM18516
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
4DNES3IV77UJ
Multiple Experiments
File
4DNFI5VLBU41
contact list-combined (pairs)
6.64 GB
-
File
4DNFIUATRW3Z
contact matrix (hic)
3.7 GB
-
File
4DNFIOF2U3HX
contact matrix (mcool)
2.45 GB
File
4DNFIJBOIRJJ
boundaries (bed)
146.01 kB
-
File
4DNFIHGWI47Y
insulation score-diamond (bw)
3.95 MB
-
File
4DNFIWJX1Y2C
compartments (bw)
205.1 kB
-
Experiment
4DNEXQ7AIQ4O
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM18516 with HindIII
File
4DNFID1SPU94
alignments (bam)
55.06 GB
-
File
4DNFIHDYKTU3
contact list-replicate (pairs)
3.01 GB
-
Experiment
4DNEXZRAD9HM
Bio Rep 2, Tec Rep 1
Dilution Hi-C on GM18516 with HindIII
File
4DNFIKDXTCFQ
alignments (bam)
72.59 GB
-
File
4DNFIHXJPBK7
contact list-replicate (pairs)
4.08 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNES3IV77UJ
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI5VLBU41
358.07m
44.416%
22.123%
33.461%
Experiment
4DNEXQ7AIQ4O
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM18516 with HindIII
File
Contact List-replicate (pairs)
4DNFIHDYKTU3
154m
42.865%
22.787%
34.349%
Experiment
4DNEXZRAD9HM
Bio Rep 2, Tec Rep 1
Dilution Hi-C on GM18516 with HindIII
File
Contact List-replicate (pairs)
4DNFIHXJPBK7
204.07m
45.587%
21.622%
32.791%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES3IV77UJ
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIOF2U3HX
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXQ7AIQ4O
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM18516 with HindIII
File
Alignments (bam)
4DNFID1SPU94
244.58m
15.141%
8.123%
8.115%
5.656%
0.275%
Experiment
4DNEXZRAD9HM
Bio Rep 2, Tec Rep 1
Dilution Hi-C on GM18516 with HindIII
File
Alignments (bam)
4DNFIKDXTCFQ
310.88m
11.143%
7.786%
10.092%
5.334%
0.338%