Experiment Set

4DNESWPXZFBC
released
View JSON

Custom Set: ENCODE Batch 1 GM12878 in-situ Hi-C

   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: MboI

2 Processed Files

Experiment
File
File Type
File Size
Experiment
4DNEX5D543VH
in situ Hi-C on GM12878 with MboI
File
4DNFIP9ADMXB
alignments (bam)
16.22 GB
File
4DNFIU585JSM
contact list-replicate (pairs)
1.45 GB

Quality Metrics

Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX5D543VH
in situ Hi-C on GM12878 with MboI
File
Alignments (bam)
4DNFIP9ADMXB
97.52m
4.924%
10.45%
0.605%
3.916%
1.576%
Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
Experiment
4DNEX5D543VH
in situ Hi-C on GM12878 with MboI
File
Contact List-replicate (pairs)
4DNFIU585JSM
78.12m
46.611%
34.15%
19.239%