Resource
| Id | TF_ChIP-seq/ENCSR000AMA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000AMA [biosample_summary="Homo sapiens HepG2" and target="CTCF"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_error: Processed alignments file {ENCFF129CNS|/files/ENCFF129CNS/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 1959659 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-human and investigated as a transcription factor is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/} ) audit_internal_action: Released analysis {ENCAN293JLK|/analyses/ENCAN293JLK/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_internal_action: Released analysis {ENCAN293JLK|/analyses/ENCAN293JLK/} has in progress subobject document {1957f40f-d9d1-465b-be12-94371b07d22e|/documents/1957f40f-d9d1-465b-be12-94371b07d22e/} audit_warning: Processed alignments file {ENCFF520WEM|/files/ENCFF520WEM/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 10128882 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-human and investigated as a transcription factor is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/} ) audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF205OKL|/files/ENCFF205OKL/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline have a rescue ratio of 1.33 and a self consistency ratio of 2.98. According to ENCODE standards, having both rescue ratio and self consistency ratio values < 2 is recommended, but having only one of the ratio values < 2 is acceptable. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF194VBQ|/files/ENCFF194VBQ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline have a rescue ratio of 1.33 and a self consistency ratio of 2.98. According to ENCODE standards, having both rescue ratio and self consistency ratio values < 2 is recommended, but having only one of the ratio values < 2 is acceptable. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000AMA | float |
TF_ChIP-seq_ENCSR000AMA |
TF_ChIP-seq ENCSR000AMA [biosample_summary="Homo sapiens HepG2" and target="CTCF"]
|
 |
[2, 434] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 11109636 | 0.35% | 46752 |
| chr1 | 964451 | 0.39% | 4113 |
| chr2 | 1038065 | 0.43% | 4325 |
| chr3 | 678105 | 0.34% | 2849 |
| chr4 | 487726 | 0.26% | 2030 |
| chr5 | 551946 | 0.30% | 2316 |
| chr6 | 672205 | 0.39% | 2794 |
| chr7 | 521327 | 0.33% | 2231 |
| chr8 | 465105 | 0.32% | 1978 |
| chr9 | 442087 | 0.32% | 1865 |
| chr10 | 493430 | 0.37% | 2102 |
| chr11 | 546065 | 0.40% | 2370 |
| chr12 | 523088 | 0.39% | 2239 |
| chr13 | 249749 | 0.22% | 1020 |
| chr14 | 394243 | 0.37% | 1657 |
| chr15 | 347078 | 0.34% | 1490 |
| chr16 | 449424 | 0.50% | 1864 |
| chr17 | 553411 | 0.66% | 2324 |
| chr18 | 226569 | 0.28% | 968 |
| chr19 | 401186 | 0.68% | 1745 |
| chr20 | 432525 | 0.67% | 1755 |
| chr21 | 111121 | 0.24% | 461 |
| chr22 | 232236 | 0.46% | 995 |
| chrX | 316777 | 0.20% | 1221 |
| chrY | 11717 | 0.02% | 40 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 46752 | 1 | 485 | 237.63 | 243 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF205OKL.bed.gz | 713.3 KB | e8a6113a4bcdd9a73d5a9c0f6ada58d8 |
| ENCFF205OKL.tabix.bed.gz | 543.32 KB | 46182d3a99172ca3f4e3dac367f0998b |
| ENCFF205OKL.tabix.bed.gz.tbi | 288.36 KB | 1176ea1c988fbc2df19e66073625b8e5 |
| genomic_resource.yaml | 3.75 KB | d4c6479a8a1f77f9a41d94844c4d8863 |
| statistics/ |