ExperimentSetReplicate

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ExperimentSet4DNESLLTENG9
released
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GM12878 dilution Hi-C experiments from Selvaraj et al (GSE48592)

   May 12th, 2017 at 4:31pm
Source Publication
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.
Selvaraj S, R Dixon J, et al., Nature biotechnology 2013

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
H. sapiens
Sample Type 
immortalized cells
Sample 
GM12878
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
4DNESLLTENG9
Multiple Experiments
File
4DNFIACOTIGL
contact list-combined (pairs)
10.68 GB
-
File
4DNFI7J8BQ4P
contact matrix (hic)
6.82 GB
-
File
4DNFI3UNF9VB
contact matrix (mcool)
7.53 GB
File
4DNFIQBWXNL1
boundaries (bed)
152.57 kB
-
File
4DNFIL4R5TFE
insulation score-diamond (bw)
3.93 MB
-
File
4DNFISY19A47
compartments (bw)
205.03 kB
-
Experiment
4DNEXBZAHAQZ
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM12878 with HindIII
File
4DNFILCG5K3O
alignments (bam)
75.65 GB
-
File
4DNFIPNVIPH2
contact list-replicate (pairs)
5.88 GB
-
Experiment
4DNEXLQ26QO3
Bio Rep 2, Tec Rep 1
Dilution Hi-C on GM12878 with HindIII
File
4DNFIOJ1GI2Y
alignments (bam)
71.26 GB
-
File
4DNFIS1QJDPA
contact list-replicate (pairs)
5.39 GB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESLLTENG9
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIACOTIGL
601.74m
25.674%
18.548%
55.778%
Experiment
4DNEXBZAHAQZ
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM12878 with HindIII
File
Contact List-replicate (pairs)
4DNFIPNVIPH2
313.96m
25.859%
18.321%
55.82%
Experiment
4DNEXLQ26QO3
Bio Rep 2, Tec Rep 1
Dilution Hi-C on GM12878 with HindIII
File
Contact List-replicate (pairs)
4DNFIS1QJDPA
287.78m
25.471%
18.796%
55.732%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESLLTENG9
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI3UNF9VB
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXBZAHAQZ
Bio Rep 1, Tec Rep 1
Dilution Hi-C on GM12878 with HindIII
File
Alignments (bam)
4DNFILCG5K3O
425.72m
9.981%
8.527%
4.959%
2.784%
0.374%
Experiment
4DNEXLQ26QO3
Bio Rep 2, Tec Rep 1
Dilution Hi-C on GM12878 with HindIII
File
Alignments (bam)
4DNFIOJ1GI2Y
400.69m
10.664%
8.553%
6.111%
2.851%
0.382%