Experiment Set

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4DNES5CWQYDL
released
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Custom Set: GM12878 in-situ Hi-C (DpnII)

   April 9th, 2017 at 5:34pm
Source Publication
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Rao SS, Huntley MH, et al., Cell 2014

Assay Description  

Experiment Set Properties  

Set Type 
Custom
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
GM12878
Experiment Type(s) 
in situ Hi-C
Modification Type 
None
Treatment Type 
None
Assay Details 
Enzyme: DpnII

10 Processed Files

Experiment
File
File Type
File Size
Experiment
4DNEX7T12MC9
in situ Hi-C on GM12878 with DpnII
File
4DNFIXC9RDV4
alignments (bam)
17.46 GB
File
4DNFI3YOU78V
contact list-replicate (pairs)
1.38 GB
Experiment
4DNEXNHE6X77
in situ Hi-C on GM12878 with DpnII
File
4DNFIHBDN5SX
alignments (bam)
23.34 GB
File
4DNFI6GHPTLB
contact list-replicate (pairs)
1.89 GB
Experiment
4DNEXAW9SYPS
in situ Hi-C on GM12878 with DpnII
File
4DNFI7A4OA9Y
alignments (bam)
22.57 GB
File
4DNFIUXFBVHA
contact list-replicate (pairs)
1.68 GB
Experiment
4DNEX17IBYLJ
in situ Hi-C on GM12878 with DpnII
File
4DNFINBX434J
alignments (bam)
16.97 GB
File
4DNFIR53NCUM
contact list-replicate (pairs)
1.45 GB
Experiment
4DNEXVL9RXOG
in situ Hi-C on GM12878 with DpnII
File
4DNFIYR3FDFE
alignments (bam)
18.9 GB
File
4DNFINOS8VK8
contact list-replicate (pairs)
1.39 GB

Quality Metrics

Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX7T12MC9
in situ Hi-C on GM12878 with DpnII
File
Alignments (bam)
4DNFIXC9RDV4
100.55m
7.102%
10.521%
2.322%
5.76%
0.334%
Experiment
4DNEXNHE6X77
in situ Hi-C on GM12878 with DpnII
File
Alignments (bam)
4DNFIHBDN5SX
136.43m
6.681%
11.243%
1.881%
4.852%
0.379%
Experiment
4DNEXAW9SYPS
in situ Hi-C on GM12878 with DpnII
File
Alignments (bam)
4DNFI7A4OA9Y
125.71m
5.804%
13.073%
1.09%
8.024%
0.38%
Experiment
4DNEX17IBYLJ
in situ Hi-C on GM12878 with DpnII
File
Alignments (bam)
4DNFINBX434J
101.69m
6.138%
9.824%
1.671%
4.075%
0.431%
Experiment
4DNEXVL9RXOG
in situ Hi-C on GM12878 with DpnII
File
Alignments (bam)
4DNFIYR3FDFE
103.18m
5.768%
12.535%
0.787%
9.051%
0.339%
Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
Experiment
4DNEX7T12MC9
in situ Hi-C on GM12878 with DpnII
File
Contact List-replicate (pairs)
4DNFI3YOU78V
74.7m
42.086%
38.993%
18.921%
Experiment
4DNEXNHE6X77
in situ Hi-C on GM12878 with DpnII
File
Contact List-replicate (pairs)
4DNFI6GHPTLB
102.79m
48.622%
32.817%
18.561%
Experiment
4DNEXAW9SYPS
in situ Hi-C on GM12878 with DpnII
File
Contact List-replicate (pairs)
4DNFIUXFBVHA
90.52m
53.572%
26.421%
20.007%
Experiment
4DNEX17IBYLJ
in situ Hi-C on GM12878 with DpnII
File
Contact List-replicate (pairs)
4DNFIR53NCUM
79.61m
39.791%
42.417%
17.792%
Experiment
4DNEXVL9RXOG
in situ Hi-C on GM12878 with DpnII
File
Contact List-replicate (pairs)
4DNFINOS8VK8
74.14m
54.522%
26.265%
19.213%