ExperimentSetReplicate

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ExperimentSet4DNES5BDII8F
released

TrAC-loop on GM12878 cells- 4 biological replicates

   February 9th, 2018 at 4:05pm

Data Usage Guidelines  


Data Use Guidelines: This is a data set generated by the 4DN Network and made freely available to the scientific community. If you are intending to use these data for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication. In your manuscript, please cite the 4DN White Paper (doi:10.1038/nature23884) and the 4DN Data Portal paper (doi:10.1038/s41467-022-29697-4), and please acknowledge the 4DN lab which generated the data. Please direct any questions to the Data Coordination and Integration Center.


Experiment Set Properties  


Set Type 
Replicate
Organism 
Sample Type 
immortalized cells
Experiment Type(s) 
Modification Type 
None
Treatment Type 
None
Assay Details 
None

11 Processed Files

Experiment
File
File Type
File Size
Notes
From Multiple Experiments
4DNES5BDII8F
Multiple Experiments
contact list-combined (pairs)
1.77 GB
-
contact matrix (hic)
662.72 MB
-
contact matrix (mcool)
544.66 MB
Experiment
4DNEXE2EER1V
Bio Rep 1, Tec Rep 1
TrAC-loop on GM12878 (Tier 1)
alignments (bam)
10.25 GB
-
contact list-replicate (pairs)
673.15 MB
-
Experiment
4DNEXAHVP5SD
Bio Rep 2, Tec Rep 1
TrAC-loop on GM12878 (Tier 1)
alignments (bam)
10.11 GB
-
contact list-replicate (pairs)
647.51 MB
-
Experiment
4DNEX15HMJS9
Bio Rep 3, Tec Rep 1
TrAC-loop on GM12878 (Tier 1)
alignments (bam)
7.49 GB
-
contact list-replicate (pairs)
327.7 MB
-
Experiment
4DNEXXRV8DHE
Bio Rep 4, Tec Rep 1
TrAC-loop on GM12878 (Tier 1)
alignments (bam)
6.52 GB
-
contact list-replicate (pairs)
314.6 MB
-

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNES5BDII8F
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIZDCXIL7
109.52m
11.512%
78.902%
9.586%
Experiment
4DNEXE2EER1V
Bio Rep 1, Tec Rep 1
TrAC-loop on GM12878 (Tier 1)
File
Contact List-replicate (pairs)
4DNFIF4ROSFQ
37.02m
15.138%
72.834%
12.029%
Experiment
4DNEXAHVP5SD
Bio Rep 2, Tec Rep 1
TrAC-loop on GM12878 (Tier 1)
File
Contact List-replicate (pairs)
4DNFI2ZOWMSI
36.32m
10.396%
80.597%
9.007%
Experiment
4DNEX15HMJS9
Bio Rep 3, Tec Rep 1
TrAC-loop on GM12878 (Tier 1)
File
Contact List-replicate (pairs)
4DNFIPD15L7F
18.63m
7.677%
85.624%
6.699%
Experiment
4DNEXXRV8DHE
Bio Rep 4, Tec Rep 1
TrAC-loop on GM12878 (Tier 1)
File
Contact List-replicate (pairs)
4DNFIXB7BSRD
17.55m
10.242%
81.06%
8.698%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNES5BDII8F
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIUVXHNNB
1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000; 5000000; 10000000
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXE2EER1V
Bio Rep 1, Tec Rep 1
TrAC-loop on GM12878 (Tier 1)
File
Alignments (bam)
4DNFIB1715GA
148.07m
3.572%
28.159%
43.265%
0.003%
7.39%
Experiment
4DNEXAHVP5SD
Bio Rep 2, Tec Rep 1
TrAC-loop on GM12878 (Tier 1)
File
Alignments (bam)
4DNFIGDGGOKK
153.29m
3.692%
25.396%
47.214%
0.003%
6.188%
Experiment
4DNEX15HMJS9
Bio Rep 3, Tec Rep 1
TrAC-loop on GM12878 (Tier 1)
File
Alignments (bam)
4DNFIHHRIQLR
130.42m
7.518%
19.154%
59.043%
0.001%
3.357%
Experiment
4DNEXXRV8DHE
Bio Rep 4, Tec Rep 1
TrAC-loop on GM12878 (Tier 1)
File
Alignments (bam)
4DNFINM4O27E
107.28m
5.556%
22.9%
55.183%
0.002%
4.979%